For the same reasons that ground level or sublevel parking does not meet the needs of (theoretically infinite) vertically scaled commercial, residential, or hospital buildings.
Increasing the number of levels dedicated to parking greatly increases the upkeep costs of the complex.
Removal of open-pavement parking, and installation of rooftop or parking level structures in vertical buildup will result in more total vehicles entering or exiting a square footprint area than before, as the area previously used by the parking lot will be re-purposed into much more lucrative housing or commercial properties.
Roadways (and associated right of ways for utilities et al) would likewise become obsolete as fewer and fewer terrestrial vehicles operate. The real-estate previously used for this purpose will be diverted toward the more lucrative industries cited above, with exception made for necessary utility right of way.
As buildings get closer and closer together (due to the no longer needed space between them, because terrestrial vehicle access is no longer a thing), ability to absorb traffic through the sides of buildings will diminish, as there will not be sufficient clearance for the vehicles to safely traverse the gaps between them.
as a consequence of the above, you end up 're-inventing" the road. Instead of an open sky theater in which these autonomous flying vehicles operate, you end up with more "tunnels" between builings that they operate inside of.
Parking and holding space becomes an increasingly burdensome thing, as buildup reaches new saturation.
Basically, all these ideas about how flying cars are going to make everything wonderful ignores centuries of humans fucking up the commons. You need to consider how, where, and why humans will fuck the commons. Any proposal that does not do that, is not realistic.