Brian McLaren puts it all very eloquently in an article that he wrote for Christian Single Magazine called "Doubt: The Tides of Faith". Here's a great excerpt...
When committed Christians come to me to talk about their doubts, one of the first things I say to them is this: doubt is not always bad. Sometimes doubt is absolutely essential. I think of doubt as analogous to pain. Pain tells us that something nearby or within us is dangerous to our physical body. It is a call for attention and action. Similarly, I think doubt tells us that something in us … a concept, an idea, a framework of thinking … deserves further attention because it may be harmful, or false, or imbalanced...
So, if you ask, “Is doubt good or bad?” I’d have to answer, “Yes.” It can go either way. Frederick Buechner expresses this ambivalence about doubt beautifully: “Whether your faith is that there is a God or that there is not a God, if you don’t have any doubts you are either kidding yourself or asleep. Doubts are the ants in the pants of faith. They keep it awake and moving” (Wishful Thinking)...
But again, isn’t that the way it ought to be? Shouldn’t a growing Christian have a growing understanding? Isn’t a vibrant, honest, tested faith worth some intellectual pain? In Finding Faith I talk about this in some detail. I describe how faith seems to grow in a kind of iterative, ascending spiral that has four stages. I call the first stage simplicity, where everything is simple and easy, black and white, known or knowable. Then there’s complexity, where you focus on techniques of finding the truth – since the scenario has gotten more complex. Then there’s perplexity, where you become a kind of disillusioned learner, where you doubt all authority figures and absolutes, where everything seems relative and hazy. I used to call the fourth stage maturity, but a friend pointed out it would be better called humility, because in stage four you come to terms with your limitations, and you learn to live with mystery, not as a cop-out, but as an honest realization that only God understands everything. You carry out of stage four a shorter list of tested and cherished beliefs that you base your life on, and a lot of your previous dogmatisms are now held more lightly. In a sense a person keeps finding faith and then becoming frustrated with it and in a sense losing it, and then finding a better version of it, and so on, maybe like a software upgrade….
That’s what has happened for me. At this stage in my life, I have sifted and re-sifted, and some beliefs I’ve had to release, while others have proven themselves as “keepers.” This is where Jesus is so wonderful and helpful to a person whose faith is in low tide, because Jesus looked at the whole religious system of the Pharisees, which was enormously complex and full of inconsistencies, and in essence, he doubted it. He sifted out a lot of clutter, and boiled all the rest down to some beautiful essentials … like loving God with all your heart, mind, soul, and strength, and loving your neighbor as yourself. I would rather have someone be sure of those few essentials, and live by them, than have them be sure of a million fine points of systematic theology, and not live by Christ’s call to love.
So don't let your doubts and questions deflate you. See them as God calling you deeper. Let Him challenge you to move beyond where you are to where He wants you to be.