Part of it is the check in process: going through the lines taking off my shoes, jacket, hoping that I've put my wedding band somewhere safe (can't imagine having to explain losing that), and then the occasional TSA feel up.
But it's more than that. It's being strapped down for hours on end. It's flight attendants that read rules as if they were just brought down the mountain by Moses and you will literally go to Hell (or federal prison) if you have to pee while the captain has the seatbelt sign "illuminated." It's that slight bit of motion sickness. It's the anxiety of baggage claim (if your bag has ever not come out onto the carousel, you know what I mean).
There have definitely been improvements lately. Mobile boarding passes rock. Economy plus (for those of unwilling to pay for first or business class) or what ever they call the cheap seats with extra legroom on other airlines. The fact that I'm writing this from 35k feet is also an improvement.
Improvements are great, but there's no way to feel like you're not trapped. I'm not claustrophobic. When I was I a submariner, I never felt trapped (at least physically) on the boat and I was there for months at a time. Maybe airlines can take some lessons from submarines - paint the interior bright green, white lights, give everyone a job. Maybe that would just work for me.
The good news is now I have less than four hours left on this flight.