The rabbit or Oryctolagus cuniculus has very strong hind limbs or legs that give him or her the force to quickly maneuver, make long jumps and swiftly escape in case of a predator attacks him or her.
Anatomically, these hind limbs are longer than the front ones and a rabbit may stand on his hind legs or use them to kick or box anything trying to hold it including its handler should he or she feel threatened and scared or thump on the floor.
Why do rabbits thump their hind legs?
There are many reasons why rabbits stomp one or both hind feet for a varying duration such as a few seconds to even hours. Some of the common message they are trying to convey include the following:
Warning of imminent danger
As prey animals, rabbits are very alert and once they sense danger, they signal other rabbits even in their natural habitats including in their warrens.
Therefore, hind leg foot thumping is a normal and natural bunny body language shown by bunnies as a means of warning other bunnies of a danger they have heard, seen or smelt. It is possible for them to also stand in their hind legs to try to get a better view.
The danger could be anything including a bird flying across, a cat walking around, a lit cigarette, any fast movement, house appliances such as the noises of blenders, fridges, car moving around, and so on. Some of these things might not pose any danger yet this pet may interpret them as dangerous.
While in a standing posture on all their four legs or tiptoeing with their ears alert, they may lift their hind legs and hit, stomp or pound them down  loudly. For some bunnies, the thumbing may be accompanied by a sound such as a squeal, a scream, or other noises.
While stomping on the ground some may also flash their tail  just before they thumb their feet on the ground and they may remain in the thumping posture until they know the danger is gone.
They are scared
Also, some bunnies show this behavior if you startle them such as walking silently into the room without them noticing you. This is a sign of fear and they are simply telling you they are nervous or scared.
Stomping is also noted in territorial rabbits as a means of warning you, other pets or rabbits invading their territory. Your bunny is simply trying to tell you he or she is angry at you, and you need to get out of his space.
When expressing their rage, the hind leg thumping may be accompanied by vocal warnings such as grunting. A lunge, nip or bite is also possible.
Showing irritation or disapproval
Also, thumping may be a message of displeasure, irritation or discomfort to you for something you have done, or you haven’t done such as feeding him or her, not giving him treats, eating his treats, or picking them.
If they do it while you try to pick them, they are warning you not to pick them again and the feet stamping is a protest.
Be very careful when your rabbit stomps. This is a sign of aggression in rabbits and it might be followed by it biting or scratching you.
Also, stamping may be a way to seek attention from the handler or other rabbits or if they “are upset they are not getting the attention they feel they deserve“ 
This is common if your furry critter is lonely and while seeking attention, he may be asking for food, treats, and so on.
A sing of physical pain
While these pets are good in hiding their pain and illness as they fear they would be preyed on, pain can make them stamp their feet on the ground. Rabbit bloat, gas, illness, and injuries could be causing the pain.
This thumping may be accompanied by other signs of pain such as your bunning grinding his teeth, shrieking, snarling and they might also bite if approached.
Why do rabbits thump at night?
A few bunny owners have reported instances of their rabbits thumping only or mainly at night. The reasons are the same ones we have noted. Probably there might be predators that pass nearby their hutches.
Don't you remember the Daily Mail story of a giant bunny that scared of burglars with thumping? Such could also be a reason why yours is stamping on the ground.
My rabbit is stamping its feet continuously
If this pet continuously thumps for a long time, you need to go give him or her some assurance. Ignoring them may make them die out of fright and extreme stress.  Rabbits may also sustain injuries on their hind legs as they kick them on the ground
You do not have to do any modifications to stop stomping. However, if it is excessive, you should consider modifying their environment.
For you to effectively interpret the reasons why your rabbit is thumping, you need to consider the various circumstances when it happens such as the presence of prey (like your dog), what you have done or not done to it, when it happens and where, and so on.
Do not punish your rabbit for this behavior as it is a natural one and a quite important way they commonly use communicating with you and others.