Homosexuality is not intrinsically an atheist issue. Some support gays, some don't. Other metrics exist as to whether a particular atheist does support homosexual issues, or not.

Statistically, atheists tend to support homosexuals, more often than not, because, once theism is removed from the equation (and thus forming a secular framework), there's no good reason to oppose homosexual marriage, within the context of atheism versus theism.

Also, atheists tend to find themselves side-by-side with other minorities in defending their rights, so we tend to be allies against many religious groups. Homosexuals are such a minority that are victimized frequently, alongside atheists.