I never got the hatred thing towards gays in particular.
For me, being straight wasn't a "choice," or a decision, I was born that way. Therefore, I can only assume that gay people were also born that way. What if, by luck of the draw, you were born straight into a homosexual World?
It certainly appears that the bible condems homosexuality, but it also condems inumerable other acts that we all do every day. And from my understanding of Christianity, all (or at least most) sins carry the same amount of weight (this will vary from demonination to demonination I suppose).
The whole religious thing will probably never be sorted out to everyone's satisfaction, but it seems like the higher ground would be to at least tolerate gays and anyone else who doesn't share your lifestyle/belief system, provided of course that they aren't harming others in the process.