Rabbits can thump for 2 reasons:
1) They are scared, “Danger”
2) To protest, say “NO!”, express anger. For example Medusa will do this after being picked up (and put down) to show she didn’t like that. Or after being put back after play time outside her room to show she didn’t want to go back yet.
In this video Medusa is thumping because she was scared of the suitcase I brought in. (Turn up your speakers, it sounds much louder in person).