Good points. But...
1. Yeah, with automated navigation and such it might actually be easier and safer to fly cars. But accidents will likely be more deadly on a per accident basis.
2. "We" could shave off costs, but the individual buying a flying car wouldn't see any of those savings. Plus I imagine during the 20-50 year transition period going from all wheeled vehicles to mostly flying vehicles we won't be able to cut back on our freeway system much. Plus we'd be divided between building mass transit, maintaining the current freeway system and creating infrastructure for flying vehicles. So I don't think there would be any cost savings for a very long time, and back to my first sentence, the individual paying for the flying car would be shouldering even more expense.
3. I don't quite follow. I imagine a flying car would have to be purpose built and that the first few generations of these that are truly mass market would be extremely expensive. So really I see us mostly going in a different direction, towards mass transit, more efficient vehicles and automated driverless vehicles.