Here's an interesting experiment...
go for a ride in a car with your favorite driver, but either lay down in the back seat, or wear a blindfold. Feel nervous? most people do.
But how many times have you ridden in that same car with that same driver and not felt nervous?
Go for a flight in a small plane on a fairly smooth day, and you won't be as nervous as you are in a large plane... why? because you can see out the windows, you can see what the pilot is doing, how he's 'driving' the plane.
I believe that the largest factor contributing to a fear of flying is not the fear of flying, but rather the fear of not being in control. Of having to trust someone else.