I know two people who are atheists and are close to me, who do not believe in gay marriage. One is a close family member, the other is a long-time friend. I don't think it is something on their list of priorities to rail against; however, one of them does vote (and very conservatively, I might add).
I could go into further detail on the matter of why they feel this way but I don't feel like it. I just wanted to be on the record of letting people know, I do know people like this and they are good people - they just don't get it sometimes. Since I have become more involved in thinking about the positive points of atheism, I have begun to challenge these two's views when the opportunity arises.
It can be hard to do that though, when someone is against gay marriage because they think the next think you know, we will be allowing people to marry horses. lol.