Between 750 and 1800 Muslims harassed and dominated the Indian subcontinent, reaching a political high water mark under Muhammad Tughluq and later again under Aurangzeb during the Mughal period. Just as Muslims mark the Crusades as a blot against Christendom, Hindus remember the depredations of Mahmud of Ghazni, who raided India for riches and slaves. This is the natural order of history, the strong gut the weak, as Genghis Khan, an ancestor of the Mughals (and 8% of "Asians") stated, "to crush your enemies, to see them fall at your feet -- to take their horses and goods and hear the lamentation of their women. That is best." This is not just a Muslim trait, it is a human trait. If you read Freedom at Midnight there are plenty of anecdotes of brutality allocated in generous dollops across the spectrum of faiths. One nightmare that rings in my mind is the story of Sikh militants breaking into a hospital, where there was a Muslim woman was giving birth, they waited until the delivery was complete and when the child took its first breath they smashed it against the wall so that its brains splattered over everyone. Insert brutality x committed by religious group y against religious group z if you want to feel some hatred.
The Muslim domination of India was not just divine providence, men of the steppe and desert generally dominate men of the plow all things being equal (by equal, I mean organized and unified nomads vs. organized and unified farming societies). That was the pattern in China, that was the pattern in central Asia, so it is no surprise that Muslims dominated Hindus for 1,000 years when sword and musket were at issue . Unfortunately, from the Hindu perceptive, these barbarians came with a high civilization of their own. The Muslims were not the first nomads to push their way down down from the Khyber pass, the Aryans, Greeks, Scythians and White Huns are a few of the many groups that entered the Indian landscape with sword and horse only to be swallowed by the green plains of Hindustan . Though the Aryans gave their language to much of northern India, and some of their blood, they were barbarians whose culture was synthesized with that of the indigenes to produce something far different from the almost Viking sensibility that one gleans in the Vedas. The Graeco-Bactrians, though possessed of a high culture, were pagans who had no philosophical aversion to synthesis and absorption of alien ideas and values. Their role in Indian history was to introduce better coinage as well as injecting an Appollonian sensibility toward depictions of the Buddha. Later, the Scythians and White Huns were fully absorbed into the Indina matrix and likely played a part in the origins of the Hindu Rajputs.
But the Afghans, Turks and Persians brought with them a religion that was in many ways the antithesis of the norms of Hindustan and would brook less synthesis and assimilation. Islam was a high culture, the Arab armed with the elan of his faith in the One God had conquered and eventually converted the Egyptian and the Persian, peoples with an ancient lineage and great pride, and later absorbed the brutal hordes of the Turk and Mongol. The Muslims who came to India, merchants and warriors, had no intention of being assimilated by the idolatry of heathen India, because they knew they had something better, they brought with them a message, they were a light unto the heathen .
Here are some of the Hindu/Muslim dualities that illustrate the dichotomous nature of the two faiths:
- Monistic/Dualistic 
- Images an aid to worship/Iconoclastic 
- Religiously sanctioned social stratification/Egalitarian in origin if not practice
- Ethnically based/Universalist 
- Wary of "conversion"/Missionary impulse
- Hereditary priests/Theoretically no priestly class 
- Organic/Revealed 
- Karma and reincarnation/Grace of God and afterlife 
- Cyclical conception of time/Linear conception, beginning with perfection in Eden and the degeneration of the original faith, various prophets, Muhammed, and then finally the Mahdi
- Oldest world "religion"/Youngest world religion
Certainly one can say that I am "cherry picking," but any Muslim that walks into a Hindu temple and is confronted by the images and statuary of the gods of that religion needs to look me straight in the eye and tell me that they did not feel in the pit of their stomach that they have walked into an alien world, that they could not smell the taint of the jahilyah. I also feel that most Muslims will feel more at ease in an austere Calvinist congregation than at a the quasi-pagan Roman Catholic mass where the "smells and bells" are emphasized. As an atheist, I myself have felt this atavistic revulsion, and I speak as someone who is well aware that my recent ancestors and distant relatives are Hindu by faith, rather than heathens who lack moral sense and capacity. Islamic iconoclasm is famous the world over, the destruction of Hindu temples in northern India was almost certainly exacerbated by the fact that many of them were wealthy, while statues within were an abomination in any case and served a good pretense . To add further to the point that Hindusim by its nature countervails the spirit of Islam, note the definition of the salutation namaste, it reflects the pantheistic/monistic philosophy that suffuses Hinduism. Its acknowledgement of the God-hood in every individual, in human beings, can be very disconcerting to the Muslim mind . In contrast to the Hindu acceptance of avatars, incarnations and 330 million faces of God, Muslims tend to view the multiplication of the nature of Allah, shirk, as a grave sin, in fact this is one point that some hold against Christians with their dominant Trinitarianism. Islam is a religion formed in the cauldron of the deserts of Arabia in the light of history, steeped in iconoclasm and submission to the One God, that exploded upon the world and swept from the Atlantic to the Pamirs in 100 years. Hinduism is a organic faith shaped by the co-mingling of many peoples in Mother India over thousands of years and characterized by a multiplicity of messages and a slow and gentle maturation from the mists of prehistory. There are just some realities about the two religions that make harmonious coexistence difficult from first principles and their subsequent development arc (first principles would be more important to Islam, while the development arc has been crucial to Hinduism).
But what about the facts on the ground? Were the Muslims more brutal than the previous invaders of India? Well, this is hard to ascertain, because cultural history is unfortunately not very quantitative in its methodology, and it suffers from sampling bias of a sort because of the nature of literacy and its uses in ages past, not to mention the sketchy nature of artifact preservation. For every brutal act of Hinducide perpetrated by the tolerant Akbar, you can find patronage of a Hindu temple by the fanatic Aurangzeb-even latitudinarian Hinduism had its period of persecution of Jains. Additionally, Hindu India has the peculiarity of being a high civilization that was deficient in indigenous narrative history (in comparison to cultures such as the Greeks or Chinese), so much of what we know of India comes from Muslims, Chinese and Greeks . The past 1,000 years are Islamo-centric in that we have a great Muslim's-eye view of the goings on in Hindustan, but we are ignorant of the simple and often short lives of the vast majority of the populace that is little effected by the defeat of their Hindu rajah's by a Muslim sultan or warlord. Muslims may record the destruction of temples with pride, as idolatry gives way to the One Truth Faith, but we may get a biased picture where a Muslim panegyrist may flatter a dead ruler by exaggerating the extent of Hindu-slaying for the benefit of the pious. These panegyrics might be recorded and used as fodder for the propaganda files of RSS activists hundreds of years in the future.
But as I said there is reason for Hindus to be angry, men like Mahmud of Ghanzi saw little in India beyond gold and slaves. Heathen India was nothing more than a collection of resources, to be extracted and mined for the benefit of Muslim rulers, who used their rents to wage wars and live lives of relative comfort. And yet that has been the lot of the vast majority of humanity since the rise of monarchies and centralized states. But, the resentment is not as great if the rulers are of the same color or faith as you, because there is at least some identification with the king as part of your kith and kin, no matter how illusory . Though rulers such as Shah Jahan, the son and grandson of Hindu women, were of India, even they displayed tendencies that showed that they were as much in Hindustan as of Hindustan. Farsi was the court language after all, while many of their courtiers were Persians, central Asians and Afghans. Babar and his descendents remained attached to their central Asian homeland, fighting dozens of fruitless wars against the Persians and Uzbeks, spilling the wealth of India in the plains of Afghanistan. Even today, Muslims in India tend to have non-Indian names of Arabic, Persian or Turkic provenance (this is true of many non-Arab Muslims, though it is not a tried and true rule, many Indonesian "Muslims" have indigenous, often Sanskritic, names). Among many Bengali Muslims, one has a "Muslim" name which is used in formal situations and contexts, and a "nickname" among family and friends that is derived from the indigenous culture .
Islam is a universal brotherhood that aims to embrace all mankind in submission to Allah. This is different from the mentality of Hinduism, which traditionally has evinced an aversion to looking beyond India, and whose Brahmin caste considered travel outside Mother India as an impure act . The rishis, Hindu sages and wise-men, were clear on the geographic boundaries of India, and Hindu kings rarely pushed far outside these restraints. In fact, the Punjab and Bengal were traditionally considered "unclean," near in proximity to foreign lands and influences, and late in their avowal of Buddhism, a religion which though an outgrowth of Indian religious ideals, transcended them . While the Dar-al-Islam is fluid, expansive, and ultimately universal in scope, India is satisfied with its corner of the cosmos.
The first principles can cause problems and confusions that are easy to clarify when seen in light of different axioms. Islam as it is defined today is by nature a missionary religion, and every believer is called to witness his or her faith, and eventually work toward the day with all humans will submit to God . Hinduism is by nature latitudinarian, Hindus speak with pride of the refugium that India has provided for Christians, Jews and Parsis . These groups entered India and became their own hermetically sealed castes, not making waves and disrupting the native cultural equilibrium, and in fact, both Parsis and Syrian Christians have religious traditions that are shaped by the caste strictures that dominate Indian life . Muslims (and later evangelical Christians) disrupted the equilibrium of Indian life, cutting into the caste divisions, and undercutting the hierarchy of social organization by appealing to lower caste Hindus with the promise of equality before Allah (Sufis), and inducing higher caste Hindus with the opportunity for advancement in the religion of rule . In the Hindu conception of salvation, with karma playing a central role, and God appearing in multiple avatars, there is no need for "salvation" of people who live in darkness, all people may see the spark of God in their own way, God is within everything. A Brahmin is born to ritual purity and a Dalit is not, while mlecchas, unclean foreigners, are who they are. Though tolerant of minorities the Hindu cultural system is vulnerable to assertive and aggressive religions because it is not designed to acquire and expand to counter inroads made by foreign missionaries (Brahmans could respond to Buddhists because the two traditions sprang fromt he same root, sharing common assumptions, rather than talking past one another). Since caste is so inextricably intertwined with the Hindu way of life, from the Code of Manu down to the tens of thousands of jatis of the present day, responding to Islam's appeal to the lower castes by rejecting some of its more retrograde practices has been difficult. Hindus can not help but feel that the rules of the game are slanted against them, not only do they not look kindly to converts, Muslims embrace them, and additionally, Islam has traditionally frowned upon or is very hostile toward conversions of their own to other faiths even if Hinduism was conducive to such acts.
-- Razib Khan
 Two points. Guns and horses were resources that Muslims naturally had better access to because of trade and communication with the community of nations in west and central Asia. It is no surprise that Vijayanagar in southern India , with access to the sea and further from the spigot of holy warriors and fortune seekers, was able to resist Muslims for centuries. Additionally, nomadic peoples tend to be more natural warriors during the age of cavalry. Even among nomads there is a spectrum of "cooking," so that nomads start to become sedentary and lose their hard edge and become prey to the attacks of their more savage brethren. So afte one group of nomads is absorbed by the sedentary peoples they have conquered they are overtaken by "raw" newcomers. The Oyrat Mongols for instance terrorized the Kazakh and Uzbek people in the 1600s, in part because the latter, especially the Uzbeks, had turned toward a sedentary way of life and had lost many of the qualities that made them such excellent material for martial pursuits in the past. The Khitai conquered China, only to be conquered in turn by the Jurchen, who were conquered later on by the Mongols. The Hunnish hordes are swallowed by the forests of Europe, then the Avars come in their wake, then the Magyars, the Bulgars, the Pechenegs, the Mongols, the Turks.... The conveyer belt ceased with the rise of mechanized modern warefare and the revival of infantry with muskets. Note how the Manchus finally put an end to the nomad menace, nomads themselves originally, using modern weaponry, taming the Khalkha of eastern Mongolia and decimating the Oyrats of western Mongolia.
 Any assertion that the Aryans were indigenous to the subcontinent will be ignored by me.
 The origin of Islam on the Malabar coast seems to resemble a pattern more in keeping with southeast Asia, as trans-Indian Ocean trade spread and connected a Muslim Diaspora.
 Hinduism is not a religion with specified doctrines clarified by a founder, though there are holy texts and writings (Vedas, Upanishads, etc.), so you can find an exception to any generalization. As a reductio ad absurdum, the Carvaka sect, which is considered Hindu by some Hindus (I personally think they are Hindu only in a civilizational sense, ie; inhabitants of India), was atheistic, materialistic and rejected the concept of karma! Though most Hindus are monistic (one grounding of reality vs. a dualism between God and his Creation), there is a dualistic strain, and though Hinduism is generally pantheistic, much of its practice and expression is practically theistic devotionalism, and some strains are atheistic. Also, as far as Muslims knowing they had a better alternative, I don't mean to imply every Muslim consciously was possessed of the knowledge that their belief system was superior, but rather, it was as a whole resistant to the assimilative seductions of Hinduism, just as the Jews in the Roman Empire, unlike other religious minorities, were stubborn in rejecting the Gospel. I think the thesis presented in David Sloan Wilson's Darwin's Cathedral has some insights into why some religions are successful, and others are not. There is more validity to his "group selection" paradigm than Rodney Stark's "rational choice" conception of why people choose the religion they choose, Stark's viewpoint is probably correct in some cases, and more so in the United States, but I think Wilson is closer to the truth in most contexts over the span of history.
 Some Hindu sects, like Arya Samaj, reject images and statues to aid in worship. Note that I am not stating that Hindus believe the statues themselves are gods, that is a common slander against them, but rather, like iconography in Orthodoxy they focus and channel the devotion of the believer. Additionally, some strains of Islam are less iconoclastic, particularly in the non-Arab world, though this is a relative statement.
 Though Islam is universalist today, there are some who claim it began as the ethnic monotheism of the Arabs. Additionally, though Hinduism today often rejects or looks askance at the concept of converts, peoples are often Hinduized over centuries, for instance, the non-Indian ancestors of the Rajputs or groups in northeast India like the Ahoms of Assam or the peoples of Manipur. But nevertheless, the two religions are different in their degree of acceptance toward converts. As an example, when a Buddhist warlord from Tibet conquered Kashmir in the 13th century, one version of his conversion to Islam has him asking Saivite Brahmins to allow him to become a Hindu, but they rejected him on racial grounds. He turned to a Muslim Sufi, and he accepted him without qualm. When some Hindus in Kerala were converted to Islam by force in the 1920s during a Mopilla rebellion against the British, there was a debate whether the new Muslims would be reaccepted into the Hindu fold, since they had become "unclean." Arya Samaj priests had to "cleanse" them because the local orthodox Hindus refused to have anything to do with them.
 The fact that Islam has no "priests" is confusing to many, and depends on the sect, as some forms of Shia Islam seem close to having a priesthood, though some of this is of recent origin. Nevertheless, I believe Islam's "priesthood" resembles Jewish rabbis, who are learned scholars in their tradition and interpreters of law rather than priests sanctified to perform sacraments.
 By "organic" I mean that Hinduism emerges from the matrix of Indian civilization, rather than being revealed from God through the conduit of a prophet or people. "Hindu" was originally just a term for "Indian," and the modern conception of it being one religion is rather new and due both to the contrast with Muslim beliefs and the arrival of the British who of course categorized the local peoples as they saw them, and the "idolaters" were quite clearly of a different faith than the "Moor."
 Aside from really weird deviants, like the Carvaka, karma is the central concept in Hinduism. Even the gods are governed by karma. In contrast, Islam is God-centered.
 Destroying and reappropriating temples is a monotheistic habit, not limited to Islam. And building one's own house of worship above the ruins is another tendency. It is rather unsurprising that Muslims who had military power chose to build mosques after destroying temples.
 Though orthodox Islam is not congenial to the philosophy behind namaste, some Sufis would have less of a problem with it.
 This needs more elaboration. There is a school of historiography that states somewhat seriously that a history of India is a history of India's culture-the states and rulers that existed in India were not particularly important. This is in my understanding discredited as hyperbole, but the fact remains that much of Indian chronology is calibrated by the visits and observations of non-Indians, Greek diplomats in Maurya India, Chinese Buddhist pilgrims during the Gupta period, and later Muslims who come to India with their own sense of linear history and a will to write down what they saw around them. Additionally, the use of perisheable wood-blocks as the medium of writing did not help historians in their attempt to find native sources of historical narrative.
 Mahathir Mohammed, Prime Minister of Malaysia, admits in Amy Chua's World On Fire that the New Economic Policy (NEP) that has empowered Malays had benefited a small minority of them while most of the "bumiputras" remain down-trodden. Some would assert than the inefficiencies that the NEP introduces to the Malaysian economy reduces the standard of living of the typical Malay! Nevertheless, Mohammed notes that if poor Malays see that some Malays can be rich, that gives them the illusion that they to can one day aspire to such wealth and keep them quiescent. Note that the removal of colonialism from certain areas, like Mexico, resulted in a transfer of oligarchies, from foreign overlords to "native" ones. To use a more explicit example, many African an elite have been just as exploitative and brutal toward the masses as the European powers, King Leopold depopulated the Congo river basin by treating the people like a cash crop to harvest rubber, but the elite of Africa are now doing the same thing, though they are focusing mineral resources.
 Razib is a mispronunciation by my kindergarten teacher of "Rajib," the Bengali variation of "Rajiv." My legal name is different, though everyone calls me Razib, largely because I don't really know how to pronounce the Arabic name on my birth certificate (neither do my parents, and neither did my paternal grandmother, who gave me the name, a pious Muslim woman born into a Bengali Brahmin family). For your amusement, I will recount the names of my mother's six brothers, Moni, Mantu, Kantu, Jantu, Rintu and Mustafa. I don't know their legal names, except for the last, who somehow escaped nick-namedom and has a decent Muslim name!
 This is a recent tendency if viewed as a strict maxim. The Chola kings of Tamil Nadu interfered in the geopolitics of Sumatra, and many of the southeast Asian kingdoms, from Angkor to Srivijaya had strong Hindu and later Buddhist influences, in the form of traders, priests and even some stray princes. Hindu Bali as well as the Hinduism of Vietnamese Chams is evidence of the past "Hindu International." It seems that Hinduism has withdrawn into a shell since the arrival of Islam with its foreign outlook and aggressive manner.
 The strong Buddhist influence in eastern Bengal is often given as a reason for their easy conversion to Islam via the Sufis, because the native populace had an aversion Brahmanical religion. There is though still an indigenous Bengali-speaking community of Buddhists called the Baruas.
 There are some who argue for pluralism. I find them hopefull, but I do not believe they are very influential, yet.
 The first Christians, Jews and Zoroastrians of India probably antedate the rise of Islam, but many of the major migrations were probably after Islam's domination of the Middle East from what I have read. The Parsis in particular seem to have left Iran because of the growing Islamic nature of their ancient homeland. The Syrian Christian community of Kerala has traditionally had ties to the eastern churches in Syria and Iraq, as have the Jewish communities of Kerala, though the Bene Israel of the Konkani coast seem more isolated (though genetic tests indicate descent from the Kohanim priestly class through the male line).
 My understanding is that Iranian Zoroastrians are far less averse to the idea of taking in converts in principle, while the Parsis tend to emphasize the more exclusive and ethnic nature of their faith, perhaps because in India, that is exactly what Zoroastrianism because in the context of the caste system.
 A recent genetic profile of Y chromosomal haplotypes in Uttar Pradesh that surveyed the frequencies of "East European markers" in Indian men found that while Kshatriyas and Brahmins were possessed of them to a high degree, Dailts were generally lacking, with Muslims in the middle. This to me indicates that Muslims might be a pretty representative sample of the whole Hindu population, both high and low caste.