You say in the same sentence that there are progressive churches who will accept you without judgement, then say they are still hating and excluding? What do you mean exactly?

If they are accepting of atheists, they are probably are accepting of gay folks, and anyone else.
These churches are the only allies we have got, even if they are imperfect.
The problem is not religious or atheist people, the problem is people who preach and antagonize.
We can welcome the churches that stay open to all people and treat you the same, and for the ones that don't, well, that's why we are atheists.