As someone who looks at life with a glass is half empty attitude I constantly waver on the edge of depression. I always see where everything falls short or the powers that be are trying to screw us over.
Translate this to the spiritual realm and I am sure you can see how it easy for me to doubt the existence of God. Even more difficult for me is the supernatural stuff that is predicted for the end times. It is tough enough to believe in the incarnation and resurrection; let alone all of the fundamentalist end times scenarios.
I can see God coming to live among us and using a method that resonates with us to redeem mankind. It is really a simple plan that all of the various denominations of Christianity make very difficult. There is a different triune God being worshipped depending on what church you show up at.
If I attend church every week and participate in the liturgy and communion I am good. When I attend a funeral at my old church and am confronted with all the crazy afterlife claims they make, I start to doubt again. They have to make those claims because their has to be a silver lining for chaining yourself to such legalism.
It is hard to sort out healthy belief from fundamentalist garbage since it is so close in some ways. Even though I have read church history pre and post reformation exhaustively, I still wonder if it all is a waste of time.
Maybe doubt and uncertainty is a guard against arrogance and intellectual laziness. If you have doubts investigate and read more about them. You will see it leads you to more questions and how you will never master any subject 100 percent.