Ken at Chicago Boyz makes an excellent observation with regard to flying cars: they aren't meant to operate over cities, they're mean to replace cities.
For all of these purposes, the flying car serves not as a means of traveling within a city, but as a substitute for the city itself! Instead of shortening the distance between people and enterprises by crowding them into a city, the skycar shortens the travel time while allowing the people themselves to live hundreds of miles away from their jobs, their friends, and their favorite shops. A few dozen houses may be clumped together in a single clearing, or a single house may stand on its own, but in either case small neighborhoods and single office buildings/strip malls/large stores will be surrounded by miles of wilderness, and people will spend most of their time endangering nothing but trees or grass if they happen to suffer mechanical failure, and enjoying plenty of space between themselves and the nearest fellow traveler.
He also observes that decentralizing our population will make our country more resistant to terrorist attacks (even nuclear weapons). Not to mention the potential environmental benefits to be had, and the psychological benefits of lower population density. I suspect most people would live in town-sized clusters of 2,000 to 5,000 people, rather than the tiny villages Ken describes, but I agree that the megalopolis may eventually be a thing of the past.