Rabbits can thump for a variety of reasons. It is thought that it’s “purpose” is to warn rabbits that are under ground of dangers.
You may have startled your bun, which would be the most likely reason why he thumped.
Fear is however not the only reason why rabbits thump. Rabbits can thump, so thumping in their behavioral repertoire. Their repertoire is somewhat limited since they cant speak etc, so they have to use a limited set of behaviors to express a wide variety of emotions, demands and needs. Pretty much all rabbit behaviors need to be interpreted in the context in which they are displayed.
How do you react when your bun thumps? You may have reacted in a way that the bun perceives as a success. If you back off when he thumps, he will quickly learn that thumping makes the hoom go away. Every time you respond to the thump by backing away, this thumping is reinforced.
I had a bun who came to realize that if he thumped in the middle of the night, the hoom (I) would get out of bed and give him a treat. Thus he thumped every night until I understood that there wasn’t actually anything wrong with him when he thumped, he just wanted his 2 am treat 😬 The solution was of course to not get up and fuss over him.
Rabbits can thump when they’re annoyed with you, f ex after nail-clipping, and they can thump out of sheer lust for life when they are zooming and binkyingv around in a room.