Can I list a few? I went to Catholic schools and was pretty God-loving until I started really thinking after highschool.
First things that made me doubt:
* The idea that non-believers will go to hell merely for not joining the club. Where's the justice in that? So I guess it wouldn't matter if I was a kind and loving person. I'm going to hell anyway because I don't believe. Right.
* When people are saved, or other good things happen, "Praise the Lord!" When disaster strikes - natural ones, no less - or if babies are born to breathe only for minutes, it's not God's fault. And if it was part of his plan, then "He knows best". That last line makes me sick.
God just can't lose.
* Don't even get me started on those who think God played a part in helping them win a sports match or some award. Starving kids, innocents about to be executed, people who walk hours for a bucket of clean water...who cares? Helping you win that Grammy was on top of God's to-do list. (Of course, this is a point against believers, not the religion itself).
* Most of all, I knew that if I ever wanted anything, I'd have to search and work for it myself. And I wouldn't have to wrack my head trying to justify and "reason" why God allowed a loved one to die. No, crap just happens in life and that's much easier to accept.