That is a tough one, a hard line to distinguish at times.
There are real issues yes, but not every church is like every other church. Because one church has a nasty pastor who abuses people does not mean all do. I know you know that, but there are people who seem to not know that.
I think it is good to address specific problems at specific churches.
X happened at first Baptist in X city, and it was wrong because .....
instead of ... this happened at a church and al churches are like this and are evil etc.
While you you are doing is good, and there are others doing good in pointing out problems as well.
there are many atheists who love tearing down the church because of the hatred they have.
CHristian bashing is very popular these days
and every single christian belief is up for degradation.
I think if you do it in a good spirit, and be specific instead of generalizing, you will do fine.
I think when people criticize the church it is a legitimate question to ask what they are actually doing to solve the problem....