Not really, because you have another dimension to expand into, so you can imagine adding as many levels as you need. Also you avoid all the obstacles that cars have to navigate at ground level (rivers, buildings, trees, etc).
On the other hand, there's some work to be done to define good copter "rules of the road". A simple solution is to say you can only go north at lvl1, east at lvl2, south lvl3, west lvl4. That would pretty much eliminate lateral collisions, so then you've only got level changes and takeoffs/landings to solve and it's done.
On the other other hand, there are bad drivers, there'll surely be bad pilots. Perhaps self-driving copters is the answer!