It may not be out of spite or prejudice, and it may very well be just what you think.

But if you go around saying Homosexuality is a sin, but your's isn't it's Discrimination.
It may be with decent intentions, but you're still treating something they are born with as if it is something bad and be forgiven for. 
It's like me saying "I think being black is a sin. I keep it in my head, and I still love black people. But being Black is a sin".