From what I've seen, Chemist_Geek's responses are more along the lines of taking issue with opinions of the "all Muslims are like that" variety. If that causes "hostile reactions," then I submit that the problem is more likely with those who are saying stupid things, than with the people who point those things out.
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It's not CG's taking issue with some of the more negative posts about islam; it is the manner in which he does so; often combative and insulting and does nothing to ennoble the debate. So, naturally, some people will respond in kind. I've been guilty of that myself when goaded and I do try not to get personal in these debates.
Also, he will not answer even politely phrased questions if they don't seem to fit his world view.
Just my observations; I'm a newbie so I don't pretend any expertise here.
You may be newer than some of us, but you analyzed that situation perfectly.