In my experience frequenting those boards as a former atheist, the vast majority of the militant atheist types were harmed more by their inability to compete in the standard hierarchies of society than they were by any particular Church or faith.
Most of them are angry at "The Man"—God just happens to be "The Man" at the very top.
I get your perspective and I will admit there are surely cases like that - I still wouldn't say it's a vast majority.
Though that raises a question. For example if you were a LGBT person in Deep South and abused over that, who is to blame? Every individual who did that (unfortunately, in the name of religion), or the Church culture who allowed for that to be norm?
And anger over church. I'm Polish, and I'm bi. The most well-known bishops were politically hand-in-hand with the previous ruling party. I would hear in public state media how I'm a part of "rainbow disease" that's infecting the country. Church would often buy land for 1 (!)% of the price. At which point can I say that it wasn't just a few bad apples, but the whole structure who allowed for things to be that way?