I've always had plenty of doubt about a lot of things the Catholic church teaches, but I was so religious I just rationalized them away. But I think what really led me away from religion was reading sites like skepdic.com and Skeptical Inquirer. They taught me how to think critically and rationally, and well, naturally my faith fell like the house of cards it was.
Christian apologetics is the art of rolling a dog turd in sugar and selling it as a donut.