One, I think, is that flying is something that is being done to us, and driving is something that we do ourselves. So the agency, the point of view is very different. Something bad happening while being passive is much more horrifying because of the powerlessness.
The other is that cars and driving environments differ a lot, while planes are much more similar to each other. What I mean by this is that it's easier to dissociate the car deaths, because that happens to some other people over there, nothing like me, but plane badness happens to everyday folk in a big winged tube, like me.
I think that if we drove the planes ourselves, the issues would be much more similar. And similarly, if everyone took the train, the bus, or a ship, and similar things would happen to a train, bus or ship, the freakout would be similar to what we see now with planes.