When I read that I see Sam Harris attributing things like "honor killings" to the doctrine of Islam as if Islam is a monolithic entity. He's equating the extremists with the mainstream and that is exactly what the islamaphobes do - insist that the crazies are the ones who have the true interpretation of islam and that the vast majority of regular muslims don't count because they aren't crazy. It is kind of like saying that all christians should be judged by the actions of the Westboro Baptists. The crazies get the headlines but they only define the fringe, not the mainstream.
FWIW, the one thing I can agree with Sam Harris on is that European integration of muslims (and other minorities) is slow compared to the US because they have less of a commitment to freedom of speech. For all of our racial problems, the US does a better job of integrating immigrant communities because we have a culture of airing our dirty laundry, of hashing out our feelings - bigotry and all - and thus working through the differences rather than sheltering people from possibly being offended. Its ugly and frequently unpleasant but in the long run I think we reach a level of accommodation a lot sooner.
FWIW, I'm an atheist who married a woman from an immigrant muslim family although I've probably been in more mosques than she has.