The Doctor doesn’t particularly care for air travel. It’s all very well for humans; in terms of getting from one place to another very distant one on their home planet aeroplanes are one of their greatest achievements. But for a Time Lord in possession of a TARDIS even the most modern and up-to-date passenger jet is still unbearably primitive.
Air travel is time consuming as well. Even in an emergency it can take hours to get where you’re going, whereas using his TARDIS he can reach his destination in no time at all.
The wonders of aviation aren’t that wonderful.