I was raised in a Catholic family -- baptized, confirmed, served as an altar boy, the whole deal.
I became an atheist when I was 16 or 17 for two reasons. First, I learned about the scientific method in high school, and I couldn't reconcile my faith in God with a lack of observable empirical evidence (and I'm aware that's entirely the point of having faith, but logic won out over superstitution for me).
The second reason why I abandoned the Catholic Church is because I started reading about the atrocities it committed over the centuries -- from the Crusades and the Inquisition right up to inexcusable and intolerable actions that continue to this day. The Vatican, even in the 21st century, has blood on its hands. In Africa, where the Church is still viewed as a trustworthy authority figure, Catholic officials are actively discouraging the use of condoms and spreading misinformation about their effectiveness at preventing the spread of AIDS (even going so far as to say that condom manufacturers purposely lace condoms with HIV). This horrible and misguided abuse of trust will directly lead to the deaths of thousands -- if not millions -- of Africans.
Or perhaps you recall a more recent case of a nine-year old Brazillian girl who was sexually abused by her step-father and became pregnant with twins. Her doctors confirmed that there was no possible way she could survive carrying the fetuses to term, so they performed an abortion to save the young girl's life. The local bishop, upon hearing of the abortion, excommunicated the doctors and the girl's mother. The child-rapist was not excommunicated. I want absolutely no part in any organization that would sanction such a great perversion of justice.
Like you, I went through a pretty severe case of Catholic Guilt because I'd been indoctrinated in the Church's teachings pretty much since birth, but I eventually got over it. Ultimately, losing the faith was the most spiritually liberating event in my life.
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