As someone -- maybe Chris Hayes yesterday? pointed out, it's always a bit silly and potentially bigoted for members of one cultural subgroup to attempt to characterize any other group of "those people" as a whole.
As Hayes and this piece both point out, we wouldn't put up with sweeping statements about all "Jews" or "Christians" being peaceful or violent or good or bad or what have you. All of "them" are not one thing or the other, period.
At the root, we can draw rational conclusions about what people DO, not who they are. A fair chunk of people in countries in the Middle East are beset by extremists with nasty ideas about a lot of things -- women, justice, religious freedom.
Funny thing is, we are beset here in the U.S. by people of supposedly different religious backgrounds who also have nasty ideas about a lot of the same things. Yes, we are more stable and have a more secular form of government, and the Crusades were a long time ago and blah and blah and blah. It's generally less extreme. But it's not like "they" have all the stupid ideas and "we" don't.
We get nowhere arguing that this or that "holy book" or the people born into one religious tradition or another are problem. No one is going to "win" a Best Religious People of the World trophy or anything.
The desire to pick winners and losers based on religious identity is a low, tribalistic one, that we supposedly all ageed was a super bad idea a while back. We are not going to eliminate or subjugate *a religion* for being "bad."
But we can talk about bad acts and bad ideas, and we can stop excusing any of them on the basis they are written in anyone's holy book. We be better atheists and Jews and Muslims and Christians.
Then maybe someday, we can all have sandwiches with Ben Affleck. 
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