All reports point to their bible. So basically they're intolerant because of the bible tells them to. Why would God do that?
Because homosexuality intolerance was taught in the Old Testament. When the human race was young was when the events in the Old Testament was written. Back then homosexuality had to be intolerated, to ensure the human race's survival. No such thing as artificial insemination back then.
Things have changed dramatically since the Old Testament days. While being gay is still a sin, Jesus taught us to not throw the first stone unless we have not sinned our selves. Being human we have all sinned in some way, it is inevitable. So if someone truly follows Jesus we should know to tolerate them at the very least, and love them like anyone else in the best case scenario. What you describe as religon hating and spreading intolerance is not the fault of religion. But the fault of stubborn people who prejudice because they do not know any better. I know many of close minded bigot non-christians here on this site. Christianity does not teach hate and intolerance if you follow it correctly. I would hope that no religion would.