Or do you really think there aren’t plenty of examples of people using religion as an excuse for violence against gay people?
Of course there are.
Ok, so my logic is sound then.
As for the other point, granted, but I’m reasonably sure violence against gay people is much more common than violence against anti-gay people, and further that religion often plays a part in it.
Atheists and atheist nations have been hateful and prejudiced as well. The difference is that atheists have been quicker to be more accepting in recent decades (as in tens of years compared to hundreds of years of intolerance), whereas religious folks have taken longer.