The fear of flying is actually more common that you think and can develop in people, who previously had no fear of flying. How so you may ask? Usually what happens is that there is an unconscious association with flying and something negative. That negative could be anything from mild discomfort to physical pain and white knuckle behavior even thinking about flying.
Fear can also be broken down into two categories - real and imagined. Real fear may occur in a scenario, where you are on an airplane and something actually happens like a small fire or sudden drop in pressure and so on. The memory of the actual event then triggers your fear mechanism. An imagined fear or phobia is one that has no traceable causes. It has somehow developed from some subtle even unknown event that your subconscious remembers and takes exception to that generally gets worse over time.
The imagined fear is by far more common – especially around flying. Hypnotherapy can readily be used in either case to lessen the association your mind (subconscious or not) has made with flying.