Firstly, I was lucky to have entered religion late in my youth, so it wasn't so embedded in me. Secondly, it was entering the military and being surrounded by so many different points of view, that I began to question my own beliefs.
"If Jesus was sent to die, why would Judas be considered a traitor? He only facilitated the plan to be carried out. He was actually doing what needed to be done." That stuck with me... and I started to question more and more and more things. Eventually, read and researched... not the bible... but trying to find physical proof these things could have occurred. I could no more not believe than believe until I had all the facts.
One thing that really showed me that there was no God was September 11, 2001. I began looking at the Bible for an answer when I read the section about David and Goliath where "God" helped David gain the strength he needed, and it made me think.
What's so special about David where God would help him, but not the people of the World Trade Center?
I understand that God gave people free will, but why would he pick and choose who to help? If he was all good as dictated in the Bible, he would have helped those people out, right?
In a different thread, I commented that it was the discovery that there was no Santa Claus that made me doubt the existence of first the Devil, and then God. But it wasn't until I read Fred Hoyle's 'The Nature of the Universe' that I realised that there were people — sensible people — who didn't believe in God. This really opened my eyes.