I disagree that those are the only two reasons.

Because there is no truly winning the nature vs nurture debate I'm only offering the other perspective.

I believe that some people naturally have a repulsion to sexual orientations they don't identify with. i.e. a straight man might be incredibly uncomfortable when approached by a gay man. This natural reaction explains why homophobia pops up regularly around the world throughout history despite massive cultural and historical differences.

However nature is pretty easily overridden by nurture. Teach someone to be accepting and they will be accepting despite any reservations they might have.

This is why I believe homophobia will never completely go away, but must continually be discouraged