Is there any difference in traveling on the ground or atmosphere?

Ground has a subgrid of 20x20 that you have to cross between cross-terraining, atmosphere is more akin to space travel, where you can go from point A to B without intermediate steps. In the end it depends on your purpose to decide which method of travel is better.

It depends on the distance you need to travel and the speed of your ship/vehicle.
Ground to Atmosphere: 1 hour
Atmosphere to Ground: 1 hour
Cross Terrain to Adjacent Square: 30 minutes (If Transport moves at 500 km/hr)
Cross a Square: 20 minutes ^

Using that information you can have a rough idea about which one is more efficient when traveling planet-side, depending on your situation and the distance you wish to travel.

Ok for me staying on the ground crossterraining is faster. Thanks for the help!

Same for everyone really. Nobody travels in the atmos layer, except maybe if it's the last click you do before bed. It's always faster to go by ground (if just crossing a few squares) or go all the way to orbit and back down (for crossing several squares).