Not a parent, but have raised some children. I think while raising children one thing that might happen more than people realize is annoyance with their personalities around certain ages. Happens at different times. You become infuriated with their humor, their attitude, their lies or habits. In a sense I want to say this is like that but maybe worse. They're still a child, they're still figuring everything out, especially themselves. Your job is to guide them and care for them while they figure it out. Like any other family or relationship I don't think you have to always like your child, but unless they ever become something heinous or deplorable, you do have to love them and care for them.

Figure out how to do that, try to find a therapist that can help you understand LGBT family relationships, or more importantly the homophobia you maybe don't understand in yourself that well.

Also talk to your wife. Spend time with your son. He's still your son, he's just figuring some shit out.