I read a lot of material by atheists, as well as, perforce, by believers. (Or at least, those claiming to be believers, most of whom seem destined to wind up on the SPLC's hate groups list.) I've seen appallingly few who manage to avoid the pitfalls of dichotomous thinking, although Amanda Marcotte comes close in this post.
But more than that, the argument fails to honor the people who actually show up, who actually give money, and who actually care about this event. Those people want to talk about religion. They fall into two camps, though many people have a foot in each one. First you have people like me, who are atheist activists because we see the horror religion does in the world and we simply think challenging it is more important than challenging beliefs in, say, fairies. Then you have people who’ve actually been the direct victims of horrible actions taken in the name of religion, or they’re close to someone who has, and for them atheist organizing is a healing thing to do. For instance, there’s a whole lot of child abuse going on in this country in the name of Jesus Christ, and people who see that and are distressed by it don’t need someone blabbing on to them about how they have to turn down the volume on their objections because they might offend someone.
But not quite. It's that lamentable tendency, which I've seen among atheists as much as any other group, to conflate "religious" with "Christian." (Or one of the other desert monotheisms. I can't tell you how many times the statement "But I'm not a Christian" is greeted with "Oh, Jewish?" as though there were no other alternative.) As if there were only one system of religious belief in the world, when we all know better. (And don't start on me about "American religious traditions" -- America being what it is, we have Buddhists, Hindus, Muslims, and followers of any number of older religions, including traditional Indians, as well as those such as Paganism that have been taken out and dusted off for new generations.)
For my own part, I just don't understand how reason and belief must necessarily somehow cancel each other out. To follow Marcotte's comments on the creationists picketing Skepticon, I certainly don't find evolution threatening -- in fact, it reinforces a central tenet of my beliefs, that all living things are part of the same whole, all from the same act of creation, if you will. I don't find that a grounding in science at all diminishes my wonder in the universe and its marvels -- it is, if anything, even more wonderful when you understand something about how it all works.
I don't see why so many people are so intent on forcing science -- or rationality, if you prefer -- and religion into the same sphere. They don't really deal with the same things, and while they have things to say to each other, neither has a monopoly on "truth," since there are different truths, ranging from factual accuracies to moral certainties, and they're not necessarily amenable to the same kinds of analysis. (Which is to say: "No -- your way of thinking is not the only way to think.")
Y'know, our brains have two hemispheres for a reason.