I developed a fear of flying the summer after my freshman year in college, when my flight from NYC to London had engine trouble shortly after takeoff and had to dump fuel and return to the airport. I was quite nervous during the incident (it didn't help that I'd read John Varley's novel "Millennium" the previous night!), although in the end nothing particularly dramatic happened, and I was well aware that a single engine failure on a Boeing 747 wasn't that a big a deal. In fact I don't recall being particularly concerned about getting right onto the next flight, which was uneventful. Unfortunately I had the whole summer to anticipate the stress of the return trip and incubate a dread of flying which ended up lasting me quite a few years. In fact I didn't fly at all throughout the rest of time at college, once going so far as to take a train across the country to visit a friend. Avoiding flying didn't help: it just built the fear up in my mind into a formidable monster. I was headed to Europe after college and seriously considered trying to take a freight ship; that's how bad it was. And while I did fly in the end, the dread I felt in the weeks approaching made my life miserable.
While avoiding flying definitely exacerbated my fear, frequent exposure didn't really work that well for me either. I flew quite frequently after college and in grad school, and it nevertheless took many years for me to get over my fear.
Here's what worked for me over the years. It was a combination of things:
(1) On the whole I associated flying with enjoyable outcomes -- in many cases, visiting my partner, who lived far away. Unfortunately, that tended to make return flights after an enjoyable visit all the more stressful! It sounds silly, but I made a conscious effort to shift my perspective a bit: both the flight there and the flight back were an integral part of the visit. I equated the "ritual" of flying with seeing my partner. It worked.
(2) I read a lot about aviation. Not just shallow statistics about how safe they were -- I'll admit went down the rabbit hole a little, learning about the physics of flight, aviation technology, meteorology, models of planes, etc. I played flight simulator games, seriously considered taking flying lessons, and so on. One result was that every flight I had a bunch of things to look out for both inside the cabin and out the window (oh, I'm on a Fokker, wonder how the tail speed brakes will work... nerdy things like that), and being occupied with those details diverted my attention (and was kind of fun besides).
(3) I learned to sort of "judo" my fear. I read up on air crashes and absorbed all the grisly details! When I got nervous during a flight, I would morbidly imagine all sorts of horrible things happening: lightning striking and setting off the air-fuel mix in the tank, the wings snapping off in violent turbulence, the engine suddenly throwing a turbine blade through the hydraulic lines, you name it. I imagined myself being pulverized, incinerated, dismembered, ... Of course all that over-the-top visualization had two effects: first, it made what was actually happening on the flight (namely, nothing much) seem boring by comparison, and second, it allowed me to confront the unlikely horrors of a crash with a certain amused detachment.
(4) The most important thing: I realized very early on that I wasn't really afraid of flying per se. I was afraid of being afraid of flying, if that makes any sense. It was the mostly uncontrollable physical response that I dreaded: the elevated heart rate, the cold sweat, the sense of doom, and so on. For years, I would still quite frequently feel that agitation before a flight; over time, it tended to be less of an issue once I was actually on board, but any little disruption of the routine (say, worse-than-normal turbulence) would bring it back. What I found, though, was that as unpleasant as the physical response was, it was manageable - sometimes it would be as simple as deep breaths and staying hydrated. Realizing that I had at least some control over it broke the positive feedback loop that was feeding the fear and eventually it stopped bothering me: I'd anticipate my heart beating faster and so on, but didn't really fear it, so it didn't end up getting out of hand.
Basically, it took a while for my fear to go away completely, but over the years it became less and less of an issue. Now I simply dislike flying because it's boring and uncomfortable, not because it's frightening :-)