I don't want to turn this into another God bashing thread, so I will just share what my experience was in losing faith.
Occam's Razor. I thought about how repeatedly we cited the complexity of life and that the only explanation could be a creator. Sounds like a simple explanation. Except that in order to create something so complex, the creator would have to be even more complex, by a factor of millions or billions.
I then realized that a creator wasn't truly a simple explanation.