I've been thinking about this question ever since I read Greta Christina's post on being an atheist in the queer community. I don't mean this to be a question of blame -- quite the opposite. I'd kind of like to understand the situation better, in order to avoid unfair expectations.
Reason #1: taking back one's faith
I suspect that there's a higher proportion of atheism in the queer population than in the general population -- that is, gay people are more likely to be atheist than straight people. You're more likely to question (and then follow those questions all the way to atheism) if God-belief isn't working for you. And being repeatedly told that God thinks you're an abomination would be a pretty strong motivation to ask yourself, "Wait a minute -- Who is this God dude anyway?"
But, really, that's the only link with atheism for the gay folks, and not everyone who questions God's existence winds up disbelieving. Some gay people take great comfort in their faith and in their traditions, and would rather question the assumption that God doesn't love them the way they are. For such people, to embrace the atheists would be like granting that the homophobes are the true people of faith, and are the ones who are qualified to pronounce on what God likes and doesn't like (in particular, homosexuality). It's too much like saying, "OK, if God were to exist, then you're right, He would hate me," which a lot of gay people aren't ready to grant.
Reason #2: goal alignment
Even if the gay people's needs don't line up exactly with the atheists, the common goals in the opposite direction couldn't be more obvious. Here's a case of harmful (discriminatory) laws getting passed -- based solely on religious justification, with no objective reasoning to back them up. That is exactly the sort of thing that is of most concern to atheists as a group.
Reason #3: visibility
The GLBT community got out there and said "We're here! We're queer! Get used to it." So now the atheists (like everybody else) are used it. With a little more visibility, people will start to get used to the atheists as well. (Though we don't have a good rhyme... Any ideas?)
Reason #3: the popularity ladder
Gay people are currently more accepted by the general population. Sure, they're almost as despised as the atheists, but that little difference counts for quite a lot when you're near the bottom of the popularity ladder.
This isn't an atheist/gay thing -- it's human nature in general. You don't improve your popularity by hanging out with the folks who are even more nerdy than yourself, you improve your popularity by telling those above you on the social ladder that you're like them, and join them in looking down on someone else. I touched on the personal-life version of this in the novella Young Women's, but it's also standard fare within and among disadvantaged groups...