The first procedure for human malfunction is often to collect leftover parts and look for the black box.
Airspace is a controlled sphere. Comparing flight to cars is futile e.g. There aren't many kids or streetracers popping up unpredictably. Most things up there happen in ballistic curves. And unless the pilot is a math genius with a quantum computer as a brain he'll be only second best in many cases.
Also there's a lot of automation going on anyways. In space travel obviously - the human margin of error is very expensive and deadly up there. But I also expect cargo flights to be automated soon.
As for passenger planes they might keep some puppets just for fun and giggles. On the other hand side it's questionable how much authority a pilot will have over his plane in 20 years or so.
Pilots are supposed to be the safety net if the machine fails - but in many cases the pilot is not capable to comprehend what's going on anyways. In fact it's doubtable that a "pilot" who's literally just a passenger 99% of the time is very helpful as his "flight exerience" is mostly just sitting there and drinking coffee.
So I'd estimate this order of automation:
Cargo planes with almost full automation: soon
Passenger flights with almost full automation: will take a while
Cars which can navigate and drive almost autonomously: will take a while
In the end it's not about if anything can happen. That's always the case. The real problem the industry faces is that they need to offer something that can be sued IF anything goes wrong. (Something other than their company)
A pilot was a good thing to have: if he messes up and survives he can be sued. And if not he's dead anyways. A computer? Not so much. The value of it's destruction is not important.
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