As a young Christian I figured that the challenge of atheism would be challenging in the beginning, but that as my faith grew and as I drew closer to God the doubts would diminish to a quiet whisper as my spiritual years accumulated. Perhaps I imagined it somewhat like hurdles in a race; as a young boy each one is a daunting obstacle that requires a focused leap with both feet. As the boy grows, the hurdles become less intimidating and become easier to cross. Eventually a good runner is able to take each hurdle in a stride that is indistinguishable from one running on flat ground.
These days I imagine it a bit more like a rugged uphill mountain course. At first the terrain is challenging, but negotiable as the boy becomes more agile. But though the runner grows in his skills, the challenges of the race grow to continue the test.
I never considered atheism a very credible idea; I subscribed closely to C. S. Lewis' idea that atheism is just too simple (from Mere Christianity, I believe). Briefly, one of his main premises is that everyone inherently knows a sense of right and wrong; therefore there must be some absolute standard that all of our moral compasses are hinting at. This idea seemed to make a lot of sense.
A conversation with my father challenged this thought though, and I did not have any reasonable response. His argument was that certainly, everyone has a sense of right and wrong, but that this is only with respect to the community. And as an illustration he noted the fact that, if a man is alone on a desert island, is there really such a thing as a "right and wrong" for this man? Um, hm. *shrug* Good point. Perhaps I am not recalling C. S. Lewis' arguments accurately. My feeling, though, is that I am left without any argument against atheism that can be gleaned simply from observation.
The other subtle leaning I have felt over the years is that towards evolution. What I mean is, the possibilty that the bible simply happens to describe those practices that promote survival of the fitest most effectively, but there really is no omnipotent benifactor. Consider the Parable of the Weeds:
Matthew 13:28-30 - "...The servants asked him, 'Do you want us to go and pull them up?'
"'No,' he answered, 'because while you are pulling the weeds, you may root up the wheat with them. Let both grow together until the harvest. At that time I will tell the harvesters: First collect the weeds and tie them in bundles to be burned; then gather the wheat and bring it into my barn.' "
I could be way off (it's getting late), but this sounds a little like natural selection to me.