Based on observation there tends to be a couple key reasons that tend to be most common:
1) There is a high degree of theological and historical illiteracy among Christians, and much of what gets passed on as popular information is blatantly inaccurate. The result of this can be that as a Christian is exposed to just how messy, complex, and inaccurate the popularized information is it leads to a rather large distrust of the "Christian establishment" so to speak. It can be very unsettling to learn that the Bible didn't just materialize, but that the ancient Church wrestled, debated, and spent large amounts of time and energy discussing the boundaries of the Biblical Canon--and that the question is still in some ways left unsettled as can be observed by differences between Protestant, Catholic, and Orthodox Canons. Related to this could be the Creationism/Evolution issue, when many churches present Young Earth Creationism so absolutely and dogmatically it can destroy one's entire world when someone raised in such an environment is confronted with real science and are left feeling like they have to make a choice between science and faith.
2) The other major issue that I think is cause is an increasing experience of religious hypocrisy, and of Christians behaving badly. When you continually are in an environment or witness to an environment that is toxic where in the name of the Prince of Peace people condemn, judge, criticize, attack, abuse, harm, and advocate general ugliness against other people. Authoritarian leadership, emotional/physical/spiritual abuse, and all sorts of other ugly and toxic things are a great way for someone to see the wide disparity between what is the supposed ideal of Charity as espoused by Jesus and what is perceived as Christianity-at-large. As such, why bother with the Christianity bit if it is so toxic and so unlike the Jesus it is supposed to represent?
-CryptoLutheran