There's an article by Asma Hasan on SFGate which talks about the trend of demonizing Islam for publicity gain:
Besides quoting the Koran out of context, these profiteers ignore the historical context of the Koran, translation conflicts, as well as overall themes and often the very next line in the verse, which exhorts Muslims to forgive those who wrong them.
By sprinkling your interview, speech or opinion article with a few Koranic verses or stories about Palestinians cheering on Sept. 11 and a "Blame Islam" headline, no one will notice your intellectual dishonesty and double-talk. But they will notice you.
I read Andrew Sullivan quite regularly and I feel that he at least makes a distinction between Muslims in general and "Islamofacists" specifically. I wonder if his readers appreciate that distinction, though. And I have seen plenty of examples of crass intolerance on the warblogs, usually phrased deliberately vaguely so that the author has righteous deniability. As well as contant repetition of false information and out of context Qur'anic references, like the virgins in heaven meme.