Alarm
Generally, a rabbit thumps as an alarm call. This means something out of the ordinary is occurring and everyone in the vicinity should pay attention. If you keep more than one rabbit, you may notice that one rabbit starts thumping and the others join in. The rabbit may thump because it sees, hears or smells something it does not recognize or trust. The thumps continue until the "danger" passes or the rabbit acclimates to the new stimuli.
Anger
Pet rabbits sometimes thump their back legs out of anger. For example, a rabbit may thump when the pet cat approaches the rabbit's pen. In this case, the rabbit is warning the cat that if it comes any closer, the rabbit will fight. A rabbit thumps when cornered to warn potential attackers to back off.
Annoyance
Some pet rabbits thump out of annoyance, such as when their human is taking too long to get their dinner, or someone is eating a piece of fruit that the rabbit wants. According to the House Rabbit Society, a rabbit may thump when you rearrange its cage.
Similar Behaviors
Sometimes instead of thumping, a rabbit flicks its back feet as it hops away from someone or something that has offended it. Sometimes a mild thump occurs while the bunny is foot-flicking. The rabbit is indicating annoyance and dislike for whatever proceeded the foot-flicking.