What possible logical reason could you have to be afraid of/hate gay people? Of course, you might not like watching it, but if you've ever seen one of those disgusting het couples that stands in the middle of a public area and start chewing on each other's faces, that's much worse (and much more gross) than two dudes holding hands.
Then again, there's the flamers, i.e the kind you just wanna slap. Being gay is a sexual orientation, not an excuse to be a freak. And I know plenty of gay guys and gals who *don't* resort to stereotypes, thank you very much.
tl:dr: No reason to be afraid of or hate gay people, but I can understand if people consider themselves homophobic because they hate flaming stereotypes.