My problem with Sam Harris is that he tends to grossly overgeneralize and then respond to articles written against him by constantly accusing the authors of "cherry-picking." I respect and tend to agree with Harris in most areas (excluding his views on military action in the Middle East and gun control most notably) but I think that he is certainly guilty of repeatedly making comments vague enough about "those people" which a lot of people understandably take to mean "all Muslims," which is both dangerous and irresponsible.
I absolutely agree with the "new atheist" movement inasmuch as I do think that organized religion is a dangerous and unnecessary evil. Religion is obviously very complex both socially and psychologically, and I don't mean to imply that all religious people are dangerous or that all churches cause direct harm or anything of the sort. But I do believe religion is something that should and eventually will be eradicated.
In regards to why the "new atheists" all seem at some degree Islamaphobic I think can be attributed to the fact that the key players all wrote books and rose to fame shortly after the attacks of 9/11. Whether the act actually swayed their opinions enough for them to assert that Islam is a more dangerous religion than any other or not, I'm not sure. But it makes sense that the violent tendencies of the religion would be a big part of what they're talking about right now.
This is an article we discussed at a recent Atheists and Skeptics Club meeting at my college that I think you'd enjoy, Tim.
Scientific racism, militarism, and the new atheists - Opinion - Al Jazeera English