Thumping is usually one of three things:
a. asserting dominance in the presence of other animals (especially other rabbits)
b. "Look at me! Look at me!" (used to garner attention of those around the "thumper")
c. a motion out of fear -- either of another animal, or a threatening situation.
In the wild, when a rabbit thumps, usually all the other rabbits stop for a bit to see what's up (assess the situation), and then either take off running away from the hungry bobcat (or whathaveyou), investigate the new stimuli, or show submission (or challenge) the dominant bunny.