Overall, I would say there are a lot more homophobes than people who hate all religious people, and that the former is a lot more acceptable in most circles!
Of course there are plenty of religious people who hate OTHER religions and religious people, but that's a rather different matter.
Some of those who do hate all religious people are just the types who hate anyone who's different from them. But many are reacting to the homophobia, anti-woman attitudes, generally far-right ideology of the Religious Right, and/or to the violence that the religious fanatics of all faiths perpetrate. Is it fair for them to hate all religious people as a result? No, any more than it's fair to hate all Muslims due to 9-11, or all Catholics due to the paedophilia scandal, or all left-wingers due to the oppressiveness of most Communist countries, or for that matter all football fans due to the partisan hooliganism of some of them. But I can see how it happens, especially in places or settings where the religious right is dominant.