Simple answer: Atheism is currently more politically correct than Theism.
Long answer: ehh... I don't really feel like getting into it right now. Basically it has a lot to do with easy stereotypes, atheist writers, and simply what the public is willing to accept.
Truth of the matter is, it's not just prevalent in Video Games, but literature and movies as well (Clash of the Titans anyone?).
From a literature standpoint I like to compare the works of Terry Goodkind and Brandon Sanderson.
Goodkind is an Atheist. Seriously, you need to read just a few pages of any of his books to figure that out. He spreads anti-religious sentiment throughout his entire Sword of Truth series. And he does it badly. Apparently he didn't think basing the entire plot on wonderful, good, beautiful atheists against evil, ugly, dirty religious nuts was enough, so he injects pages of anti-religious monologues into every book. It couldn't be anymore ham-handed if he tried.
Sanderson on the other hand... well, to be honest I'm not sure what his religious views are. I found out recently that he teaches at Bringham Young University (you know, that Mormon place that Stephanie Meier went to), and I was honestly shocked. Religion plays a sizable part in all of his books, but it's not the typical role you usually see. He doesn't play it up as a great wonderful, life-saving thing, nor does he cast it in the same light as Goodkind. Rather, he generally paints a fairly accurate picture of how the various religions would effect the worlds they're in, both positively and negatively. You never get the feeling that he's trying to say that religion is good or bad.
Also, he doesn't limit himself to Christianity as a template. One of his latest books, Warbreaker, actually featured a religion that closely resembled Greek Mythology. Even if his writing, plot, and characters weren't top notch (and they're among the best I've seen) I would still like him just because of the way he treats religion. He treats it with respect, but also with a critical eye for it's failings.