Regarding the atheists in question, I remember running into one of Myspace, who was so proud to have voted for Prop 8, because he thought gays were disgusting.
I'd be willing to assume that most people who are against gays are so because they can't stand the thought that a man could possibly enjoy doing *those* kinds of things with another dude. Christian fundamentalists, in case you haven't read much of their material or heard them on TV, are obsessed
with gay sex.
The scripture verses and the Church pronouncements are probably more the result, rather than the cause, of that ancient fear of something different. So many straight men it seems think that every gay man desperately wants to tear their clothes off and fondle them. I can't speak for women or lesbians, I don't think we've heard from any yet in this thread. It's a matter of fear, immaturity, and ignorance. Religion isn't the fire, but it can surely feed the fire!
And to make things more complicated, there's bigotry within the LGBT community, as well. There's racism, elitism, all the same problems that exist in the general population. Some gay Christians quit talking to me after I "came out" as a pagan who practices witchcraft (speaking of another group that is often misunderstood and discriminated against...). Some gay people don't like transsexuals. Humanity is complex, and, well, just read my Dutch proverb below.