For starters, it is highly unlikely the urban planning mistakes of the 60s where downtowns were flattened with freeways will be repeated. We're already seeing cities tear down or bury existing freeways to correct these mistakes. Cities from LA to Atlanta are investing in mass transit and are working on getting more walkable and dense.
I predict that self driving cars will actually be a big boon for cities themselves as it would now be easier for city dwellers to visit transit inaccessible destinations or shopping trips that require a car. Zipcar, Car2Go, Enterprise's car rental club and the like are already bridging the gap, but self driving cars would help those who can't drive such as children or the elderly or even those who never learned to drive.