Assuming flying cars travel at the roughly same altitude as helicopters, even if I didn't take all of the above into account, I have serious doubts as to whether autopilot could handle flying through Manhattan by itself.
There do exist personal flying devices for the ultra-rich. But if you look at how inefficient our current system is and try to put as many planes in the sky as there are cars on the ground....not looking good.
Plus, imagine you live in NYC or LA. You'd barely get any sunlight on the ground with all the planes in the air. I thought flying cars would be cool too. Then I looked at traffic conditions in LA and said "If this is the best we can do on the ground, then I don't want to see flying cars in my lifetime. The Futurama tube looks much more practical."
In that case, manual driving will be mostly like sailing a ship. Equipped with a gps, the car can maintain a course. And with a radar with a sufficient range, it can alert incoming bogies so that user can take proper action...