Does the tractor beam only work in space? Or, is it possible to tow a ship from a landing pad, take off, go into space, Quantum Travel, enter a planet's atmosphere, and finally land while towing another ship?

The Tractor Beam can be used in any location, however the environment will affect the difficulty of maintaining a capture of the target item. Another one of the original design aims was for the SRV to act as a tug ship to help larger ships get from a planet's surface back out into space.