Note: this post is inspired by a recent post by Cephus about a challenge from a Christian.
It's not terribly uncommon to come across a religious person who thinks that I am an atheist because I have been harmed by the church in some way. They will often think I am an atheist because I am angry at God, because I have seen Christians do terrible things, because I think my entire childhood was somehow damaged because of the inclusion of the religion. They will then challenge me to put aside the painful emotions associated with these things and consider returning to God.
I was angry, very angry with God and religion in general. This anger led me to question everything and look for the truth of the matter to the best of my ability. I investigated the real source of my belief in God and thought about what would have happened if I had been born in a different part of the world, or at a different time. I looked for any proof of God I could get my hands on and tried to analyze if I thought they were worthwhile. I talked about these matters with as many people as I could. Ultimately I have concluded that there are no good reasons for believing in God. My own reasons for believing were all based on the fact that I had been told these things by everyone around me since birth, and the same was clearly true for all of them.
So back to the initial question, have I been harmed by the church? Absolutely! Am I an atheist because of that harm? Well yes, but probably not in the way you mean, it's not a simple connection. I was harmed and therefore motivated to seek the truth about religion, further, due to the anger I felt for the church, I was motivated to keep looking into things for about 10 years until I was satisfied that I had seen and rejected pretty much every argument out there.
In the Christian challenge linked at the top, he asked atheists to put aside their emotional baggage and look at the evidence. But for me, and many other atheists I've talked to, the emotional baggage is what motivated us to look at the evidence in the first place. Emotion played a big part in getting us started, but we have already answered this challenge on our own.