For me it was going to a Catholic high school. I was all well and good with the eucharist being a metaphor and what not. But then when I learned about transubstantiation, and that we were suppose to believe when the priest said the magic words those wafers and wine literally, and I mean literally, turned into the body and blood of Christ, I was out. I started questioning lots of stuff from there and eventually found myself moving toward deism, then agnostic, then finally straight up aetheist.
I kept getting scolded when I used to ask how many Jesus meat and blood do we need to consume to get into heaven. Your post reminds me why I chose to be quiet about my growing atheism as a teen.