My doubts about my faith came only after I started reading the Bible on my own without the "guidance" of my church to tell me what parts to read. The Christian Bible is a book. It may have even been considered a good book by the standards of the time it was written. But to truly be a Christian, you have to believe that the Bible is "the word of God" or "inspired by God." And if anyone reads the entire book and can tell me that they believe everything in the Bible, then I have to dismiss that person as being illogical and/or ignorant.
To someone living in times that the Bible was written, I can see how they could believe most of the stories of the Bible. After about the year 1700 or so, I could see how they could believe some of the stories of the Bible as being true. But to anyone living in our "age of enlightenment" of science and human knowledge, I just can't see how they could believe any of it as being the "Truth".
Upon reading the Bible, it gave me real doubts about my religious beliefs. I contacted a priest at my local church to help me sort out my "evil thoughts" about the Bible. I told him how the story of Noah's Ark had to be false, talking of taking every species of animal into the Ark with only himself and 5 others to round up, care for, feed, dispose of waste, etc. There are numerous other reasons to disbelieve the story of Noah, some of which I brought up to him (not even taking into account that God destroyed every living human, animal, plant, etc on the planet besides the Ark inhabitants.) He was pretty logical by explaining that most stories of the Bible are parables and not meant to be taken literally (which leads to other issues of doubt in itself.)
I also mentioned some inerrancy and contradictions I noticed during my readings. He shrugged them off as items like "lost in translations" of the Bible, the "human errors" made during writing the Bible, making sure you are following proper context of the verses, and other crap. If anything, these meetings brought my faith into more doubt than before. I assume this priest was not used to defending the Bible. I bet I could have received better explanations from a Jehovah's Witness elder, as I am sure they are on the defensive a lot more and have prepared answers from a checksheet or FAQ they have from The Lighthouse.
Thus, the Bible ended up being the reason I doubt my religion. Ironic, no?