Well, the obvious one is the Dawkins quote on the airplane, already treated in ways I agree with by SilasBarta. More generally, I am troubled by atheist attacks on the idea of religious tolerance - Sam Harris says it's "driving us toward the abyss". I mean, really, if you find yourself nodding along to a pro-intolerance rant from Jack Chick then maybe you want to ask yourself some questions.

Even so, I, like Sam Harris and Jack Chick, think that Islam is awful and needs to be resisted.

Edit: Bleh, this comment came out wrong - it's more condescending than helpful. The subject is probably too complicated to deal with here. Basically I think religious tolerance has a fairly good track record and I'd want to be very careful in tinkering with it.