Below is a great article that I came across in the New York Times in which a student reflects on how his college experience led him to deeply doubt, and almost lose, his faith.  Tim Keller, in the introduction to his book The Reason for God says:

"A faith without some doubts is like a human body without any antibodies in it.  People who blithely go through life too busy or indifferent to ask hard questions about why they believe as they do will find themselves defenseless against either the experience of tragedy or the probing questions of a smart skeptic.  A person’s faith can collapse almost overnight if she has failed over the years to listen patiently to her own doubts, which should only be discarded after long reflection."

Wise words to go along with this article:

What My Faith in God Looks Like

By DUSTIN JUNKERT

I grew up quietly and without thought. My mom was a secretary at the Baptist church, and I led the worship team senior year of high school. My youth pastor was one of my best friends. I believed in God and my parents, my friends, and the four walls of my house. All things were within reach, simple and inspiring …  

Eager to continue my spiritual journey, I went to a private Christian college in Oregon complete with a lifestyle contract. Freshman year, I met Frank, a lifelong philosopher. He was a couple rooms down from me. He asked me all sorts of wild questions I had never thought about before, like, “Well, why do you believe that?” Everything I said that year, Frank would ask me that question. Then I started asking myself that question about every thought I had …

I took a class called “The Problem of Religious Diversity” … It never occurred to me until then that people who believed something other than Christianity had the same reason for believing their faith as I did for believing mine. How about that?

I ran into an old Sunday school teacher sophomore year and told him I’d been thinking that maybe it’s not true that everyone who’s not a Baptist will go to Hell. He looked me straight in the eye with saintly gravity and said: “The Bible is very clear: if you believe that, you aren’t a Christian.” … [What he said] put me in a state of fear at first, then repentance, then confusion, and lastly anger. I rebelled from the religion that contained all the smallness of my childhood. I cursed my Baptist teacher [and] God … and fled to Russia for a study-abroad semester …

The first person I talked to there was Dan, a student at GraceCollege in Michigan. He immediately asked the last question I wanted to hear: “So what’s your faith look like?” I went cold. I wanted to bleat my usual Jesus-story and be done with it, but the ice on my ribs wouldn’t let me lie. I reluctantly collapsed and told him that honestly, I didn’t know anything anymore and nothing was real. Turns out, Dan was in the same place I was.

Together we raved and doubted and yelled and trembled all semester long. We felt the black blood of Dostoevsky and descended the dark stairs of Derrida and Sartre. Some nights, we would just sit across from each other and stare, estranged by the cold of a new, uncertain world. After one of these nights of existential fog, as I got up to go, I turned to Dan and said, “The only meaningful thing left to do in this world, it seems, is to sit quietly with a friend until dark and then say goodnight.”

Then, on a snow-gray Russian day, riding a packed bus, a song came on my iPod that froze me in time. In a sense, I’m still there on that bus listening to that song with watering eyes. It was a song called “Clouds” by As Cities Burn that said: “Is your god really God? / Is my god really God? / I think our god isn’t God / If he fits inside our heads.”

…  I snapped and everything came undone. I resigned entirely. God won’t fit inside our heads, and if He does, we’re missing something. And I knew all I’d been waiting for was to know that to admit doubt was not to lose faith. A few simple lines of an Indie rock song pushed me to see hope amid uncertainty.

It snowed continually my last two weeks in Russia. I met Dan one morning at a small cafe, Biblioteca, where we drank bottomless black tea and watched the snow pile up on the street. He said he had prayed the night before. I said I was ready to step back into a church.

[In church the next day], I wrote in my journal, “God, see that I’m trying.”  It was the first time I had prayed in more than a year.