Most of us started off believing in Santa and ghosts. And then there was that moment that said... maybe not. Not necessarily comparing the two, but I think there are parallels for non-believers.
For me, it was considering the idea that maybe the afterlife is wrong (this started in roughly 5th grade). It terrified me (I stayed up for hours on end tormenting over it, before realizing how much of a non-concern non-existence really is months or years later), but I couldn't find any evidence that afterlife existed or was plausible.
But the reasons doubt starts are legion (no religious implication intended). Perhaps you saw that there are many religions, and no one could be right. Maybe you felt the moral ideals of the whatever text were dubious. Maybe the concept of God was suspect. Maybe you felt that the answers in your religion were wrong scientifically or didn't add up. Maybe you saw people using religion for oppositional reasons. Maybe some religious story was just silly to you. Maybe you saw darkness in the world God shouldn't allow. Or someone told you AIDS was God's punishment and that didn't sit right. Hell, maybe your parents didn't believe to begin with.
So non-believers. What was that first little nougat of questioning that blossomed into your current ideology?