I found few signs of London-style radicalism among Muslims in the United States. At the same time, the real story of American Muslims is one of accelerating alienation from the mainstream of U.S. life, with Muslims in this country choosing their Islamic identity over their American one.
Emphasis mine, which I think rather undercuts the headline. We ARE as assimilated as you might think; we are not a radical community. The real complaint here seems to be the issue of Islamic "identity". I see no evidence in the article that muslim americans are "choosing" their Islamic identity "over" the American one; in fact if anything there is an ongoing synthesis of the two, which is really the entire point of America. The truth is that yes American muslims are religious, but so are Christians here by and large, more so than in Europe. Few would argue that Christian Americans are choosing Christian identity over their American identity, after all. Muslims in America do not have to be Irshad Manji-style "refuseniks" to be moderate; if anything the history of America teaches us that here (and almost exclusively here!) can the persecuted peoples of the world find sanctuary to practice their faith as they see fit. American muslims do not and should not have to be secular in order to be moderate.
The truth is that muslim americans are a different demographic and have a different history than their European counterparts. I discussed this issue at length in an earlier post titled "muslim citizens, not citizen muslims" and provided quite a few links therein that address this point. Also see publius' comments on the WaPo article above, in which he makes much of the same economic and class-based arguments.
However, the sense of alienation that Muslims feel is a very real thing. What do you expect when we have talk of muslim-only airport lines? For the most part American muslims have borne the increased scrutiny without complaint. We do as a community understand why we are being singled out - but that doesn't take the sting out of "flying while muslim" in any way. But is alienation and resentment equivalent to anti-assimilation? No, though they certainly could be the seeds for it in the long run. However I have great faith in America and I do not think this will come to pass.
The whole issue of identity is really not as critical as that of modernity. Its reconciling tradition with modernity that is tricky. We all have multiple identities and we rarely "choose" one over another, but the conflict between modernity and tradition is sometimes trickier to navigate. The way in which my own community (the Dawoodi Bohras) achieves this feat was nicely described by Jonah Blank in his book, Mullahs on the Mainframe, of which you can read an excerpt here and which I myself reviewed here.