"Because God said so" didn't cut it for me as an explanation. And the more scientific education I gained, the more sceptical I became that this amazing universe had been designed by, and was being controlled on a minute level by, some single entity. The maths of how one person could control so much just doesn't make sense.
It also bothered me that God seemed so anthropocentric. I couldn't understand why every other species was apparently far less valuable than humans, and why it was okay to wreak havoc on them for human purposes. Nor could I understand why God was seemingly so arbitrary in the way he (because God is always a man!) allowed things to happen, both good and bad.