My relationship with the Christian religion is a long and conflicted one for many reasons. If you want to read the "condensed" version of my journey, you can find it on my blog referenced in my profile here. But, in short, I've struggled with many of the same issues that others have mentioned in this thread - hell, the Bible vs. science, immoral/hypocritical Christians, horrible images of God, bad churches, etc. For many of these issues, while I experienced some cognitive dissonance from them, I simply kept them on the back burner of my mind for further study. After all, I knew enough to know that I didn't know everything.
So though many of these things were "pebbles in my shoe," I kept on walking in the mainstream interpretation of the Christian faith.
But the breaking point came 8 years ago when we were attending a Bible Church and I was called out of worship service to come help with my son who was 4 years old at the time. As I entered the hallway to where the Children's Church was being conducted, I heard my son wailing and I wondered what he could have hurt himself on. When he saw me, he ran to me, crying, "Daddy, why would Jesus burn me? Why would Jesus burn me?" He was hysterical with fear. I tried to reassure him that Jesus wouldn't burn him and had my wife take him out to the car for further comfort.
I asked the Children's Church teacher what had happened and, in brief, she had shown the kids an artist's rendition of hell, with a man engulfed in flames, his arms raised to heaven, crying out for mercy to a god who would never hear or answer the cries. I was incensed and told this teacher that 1) Jesus never threatened children with hell and 2) it was an inappropriate subject for children. She replied that she did not want the blood of these children on her hands, that she had a duty to God to warn them of what would happen to them if they did not accept Jesus as their personal savior. Despite her "biblical argument," I still felt she was in serious error of presenting this to children and went to talk with the church elders about the situation. They stood behind this teacher and said that what she taught was biblical, scriptural and that the truth should be taught to all, regardless of age. I disagreed and we left the church.
This incident was the straw that broke this camel's back. I had to find a new way to interpret my faith in God or leave the faith altogether. For me, I know that God is real for my own reasons, but I don't trust the teachings of the church or of Christianity as a whole because, to me, they don't necessarily line up with the kind of compassionate God that we see in the life of Jesus. I am proudly a "cherry-picker." We have to be this way in all of life, discerning right from wrong and better from good. This applies to religion also.
I am no longer a mainstream Christian because I concur with what Ghandhi said about Christianity, "I like your Christ, but I don't like your Christians. They are not very much like your Christ." It is, of course, a blanket statement. There are many good and loving people in mainstream Christianity. But, to me, it is a religion grounded in fear and boundary-setting, not in love and freedom. Jesus said that perfect love casts out all fear and that the truth would set us free. If we live our lives in fear and bondage, maybe we aren't truly seeking or walking in truth.