Autonomous systems are great when things are going well, but at the end of the day they fare very poorly in edge cases sometimes with catastrophic results. When you’re driving a car you usually follow traffic rules and stop lights to get to your destination safely. In an airplane there’s constant communication and things change frequently based on weather, traffic, emergencies, etc. I can’t count the number of times ATC has repeated back an incorrect call sign. As a human we know it was probably meant for us and call back to confirm. Would a computer do that? Even if we used datalink communications then ATC would now have a much higher burden. Also human pilots would lose the situational awareness of hearing instructions for other aircraft on frequency.
Then there’s the question of— in an emergency situation is the computer going to be able to make the right judgement calls? What if its sensors are iced over/inop?
All in all, while technologically I feel this could have been pulled off yesterday, I doubt we will see fully autonomous aircraft operating long routes in controlled airspace anytime soon.