Flying is different because airplanes have floors under them, and the windows are too small to get the sensation of falling out of them.
I have a certain yet controllable acrophobic reaction to heights. I write it off as a sincere respect for gravity and all it implies. But I have a very difficult time getting close to edges of cliffs or peering over really long drops.
One of the hardest things I ever did was that bungee jumping thing some years ago off a bridge up in the mountains. Eric, my bud that I went with... was also into skydiving... which I'm not. He said that the bungee jump was magnitudes more terrifying than skydiving. When you're skydiving the ground is a long, long, long way away. When you're bungee jumping the rocks that you're going to bash your head against are RIGHT THERE and you can SEE THEM.
Its funny, but while the bungee jump was terrifying beforehand, once my toes finally left the bridge and I started falling... the sensation of fear *completely* disappeared. It's like there's a mechanism in the brain that clicked on a said "Well... nothing we can do about this now... may as well enjoy the ride... " :-)
If I sit on an inside seat in the back of the plane facing forward, and I look up and see all those people coming on board, in between me and the exit, I start to lose it. I begin contemplating crawling over the people between me and the aisle.
If I sit up front, on the aisle, those reactions are much diminished.
If I fly Southwest, and sit on one of the rearward-facing seats, I have no problems at all. NONE.
I read an account by a AH-64 pilot who said flying at night with NVGs was less nerve-rattling because the squirrels were asleep by then, so you didn't see them running around in the trees, eye-level with you, like you did during the day.