There actually is no paradox if you think of this way:

Be tolerant of ideas that harm nobody.

Be intolerant of ideas that harm others.

“I’m gay.” <- Tolerable.

“I’m not gay, so I won’t date men.” <- Tolerable.

“I’m not gay, so I think we should kill all gay people.” <- Intolerable.

Beliefs and personal convictions muck that up a bit though.

There's a sadly significant portion of people who truly believe that being gay is hurting other people.

Whether they believe it only because they were told to or for some personal reason, they believe it nonetheless.

A gay person existing doesn’t actually literally harm anyone though. A homphobe shouting slurs at a gay person, excluding them from vital social, economic or whatever activity or beating them up does very concretely harm someone. It’s not that difficult.