Well, for one thing, too many people just can't view homosexuality as being 'natural'. They have to view it as an abomination, something to be feared and stamped out. Because it's different. Because "those people are not like US!"
In short, it's ignorance and superstition and dogmatism, in varying combinations. And besides, the Bible says it's okay to kill "those people". You know, the same places that say it's not right to eat ham or shellfish, or to wear clothes of blended fabrics, or to get tattoos. Yeah, God doesn't like those things, either.