The first thing to understand is that fear is a natural and normal human 'negative' emotion. The purpose of negative emotions is to tell us that something isn't quite right; an indication that we need to take some kind of action.
In the case of fear, the message is 'danger'. While we are born with fear of loud noises and fear of heights 'pre-wired' in our nervous systems, and all other fears are learned from 'experience'.
The catch is, our mind is so powerful, that the 'experience' doesn't have to have been real, it could just have been vividly imagined. (That's why you can get feelings about flying just by thinking; you don't have to actually be there).
Learned fear is an important survival mechanism, but just occasionally the wires get crossed and we learn a fear response for something where it doesn't belong – where there isn't a significant danger – and Aviatophobia can develop.
The Root Cause
The root cause of Aviatophobia varies from individual to individual, and whilst no two individuals are the same, most fall into one or more of the following categories:
A Single Traumatic Incident:
A highly stressful or frightening real event at which, instantaneously Aviatophobia is created. Similar to, say, a child being bitten by a dog and developing an immediate phobia, a single traumatic incident is a one-time experience at which there is such extreme fear - even if only for a moment - that the nervous system 'learns' to associate fear to help the individual avoid such situations in futre.
The initial fear, by the way, may be nothing to do with flying. We often hear from clients that the problem started at a time when they were under extreme stress for something completely unrelated, but the mind somehow associated the negative feelings to flying anyway.
An Associated Traumatic Experience:
This is where the individual does not directly experience the fear, but 'associates' to someone who does, either in a real situation, or, more rarely, when watching someone in a movie - or even a dream - experience a traumatic event.
A Slow Build:
A slow build occurs when a mild case of Aviatophobia escalates over time to become a severe one. What is happening here is that the individual is 'accumulating' fearful associations to flying, so that the evidence used by the mind and nervous system is becoming increasingly irrefutable that fear is the appropirate emotion. That means that anxiety isso it is created automatically in anticipation each time... creating a self-fullfilling prophesy.