I flew from Hamilton to Ottawa a few weeks ago... and MAN, it sucked.
First off, the flight is only 30 mins and they don't even reach max altitude!
When I landed, it took my ears 3 hours to feel normal again. Damn ear fullness.
I did everything I could to keep my e-tubes popping...
I used to fly ALL of the time to, with no problems.
I'd say that flying can make your symtoms worse, but not the actual TMJ.
The search for a diagnosis is long and painful...