while I'm not on the staff so I don't know the official reason, this still makes perfect sense to me just as a player. On the ground you have trees, buildings, mountains, and other random outgrowths that you have to maneuver around. Plus there are probably laws against creating sonic booms at ground level due to the problems it can cause for populated areas.
In the atmosphere you suffer none of those problems and therefore are free to go as fast as you want. Just think of the speeder chase scene on Endor in the last Star Wars movie. The speeders weren't actually going that fast compared to the speed of even say a modern jetplane, yet riders were constantly dying from collisions against trees anyway.
Also is important to note that cities have "speed limits" of 200 km/h, so you are capped to that speed within cities, regardless of your ship or vehicle's maximum speed.