Agree with a lot of the guys above. Hours and hours in an aircraft, height never an issue. Climb a tall building/tower/bridge etc and the rear end starts to twitch.
Strangely, I experienced the same feeling once while in an aircraft. I was orbiting over a cooling tower on the south bank of the Mersey and decided to look down inside it. Instantaneously I remember feeling extremely glad I was not standing at the top of it, yet as soon as I looked away from it at anything else the feeling totally disappeared. It was one of the most bizarre experiences, and I'd recommend that other people see what effect this sort of thing has on them.
I've come to the conclusion that if I'm enclosed, ie. in an aircraft, on the London Eye, actually inside a building then I feel safe and secure, whereas if I feel exposed to the potential of a fall then I start to be concerned - probably 'bathophobia' in light of the above.