Daylight Atheist lists the "biggest challenges to remaining Christian," as compiled by evangelical blogger Peter Enns. The points are listed here, in bold and italics, and my own thoughts follow. As I was a liberal Christian, not a fundamentalist one, some of these had more of an effect on my long, slow deconversion than others:
1.The Bible, namely inerrancy. This was less of a problem for me than it would have been for an evangelical, as I never believed in the inerrancy of the Bible. When I was a child, my Episcopalian mother, who had also been an English teacher at the local college, would often rant that the creation story was clearly intended as a metaphor, and would complain that fundamentalists "had no sense of poetry." When I became a Lutheran as an adult, believing in the literal truth of the Bible from beginning to end would have been way too much for me to swallow. Fortunately most ELCA Lutherans don't believe this anyway. I did have some issues, though-- as I've said elsewhere, the difficulties of trying to explain to my oldest child why I took some parts of the Bible as literal truth and not others eventually caused me to admit that there was no real logic in my position. In some ways it may be simpler to be a Biblical literalist-- "this is all the perfect, inerrant Word of God" may be an easier logical position to defend than, "Some of this is just stories told by unsophisticated Bronze Age nomads, but some of it is Absolute Truth." Either way, it can be a stumbling block for anyone who allows logic to override their faith.
2. The conflict between the biblical view of the world and scientific models. Again, never a huge issue for me, as I never took the Bible to be literal, and never believed in a 6000-year-old universe or a real worldwide flood or anything like that. I did find myself with a logical problem when it came to evolution, though. If evolution is really directed entirely by random natural selection, then God could have had nothing to do with the development of the world at all (save possibly to put it in motion, as deists believe). If God directed natural selection, on the other hand, then the evolutionary theory was in fact flat-out wrong, as it wasn't random at all. In short, I found it impossible to reconcile natural selection with the idea that God had designed this world, and humanity, deliberately. Also, it became more and more obvious to me that humans could have had very little to do with the world's existence, since we showed up many billions of years after it was created. This suggested that humans were not high on God's to-do list, if he even existed.
3. Where is God? A number of you, largely in emails, wrote of personal experiences that would tax to the breaking point anyone’s faith in a living God who is just, attentive, and loving. This was the big one for me. As my husband lay dying of cancer in the hospital, my pastor tried valiantly to explain to me why a decent, kind, gentle man with four small children would be stricken by cancer at a young age. "Original sin" and "the Garden of Eden" was the best he could do, none of which made any sense to me. First of all, no Lutheran I knew believed in the literal truth of the Garden of Eden. But assuming he was speaking metaphorically, and merely meant the general sinfulness humans are prone to, that still didn't explain why God would strike down this particular human. If it wasn't God's hand at work directly, then where was God? Why didn't he intervene? What had my good, hard-working, church-attending husband ever done to deserve a slow and painful death by cancer, any more than anyone else did? The obvious answer was that he didn't deserve it, and the realization that it was simply random chance eventually helped me make sense of it all, far more than belief in God's supposed plan for our lives did.
4. How Christians behave. It bothers me now, but it didn't bother me much then. I had a lovely church community that helped me through my husband's death, and they were all pretty nice people. I rolled my eyes at the fundamentalist ideas I read about, but thought of them as a small, radical fringe group without much real effect on politics. I am more aware of their influence on public policy now, and it worries me, but it had no particular effect on my own deconversion because I honestly wasn't paying enough attention.
5. The exclusivism of Christianity. As a liberal Christian, I worked my way around this one. I never wanted to think that nonbelievers were going to hell, nor did I like to imagine that the presumably merciful God of Christianity would allow it. I felt that the assurance that "with God all things are possible" meant that everyone would be saved in the end. After all, "for God so loved the world that he gave his only son..." so naturally if he loved the world that much, everyone had to wind up in Heaven in the end. Again my teenaged daughter came to the rescue by pointing out it was Jesus himself who said those who didn't believe in him would go to hell (which he repeatedly describes as a place of fire and torment), and if I didn't take Jesus' words literally, what did I actually believe, anyway? I eventually concluded that the answer to that question was, "Not much."