I firmly believe your rabbit does understand what you say, I know that ours certainly did, and thumping is the rabbit equivalent of sticking your tongue out when he's cross, irritated, or indeed as a warning.
However, I found a rather interesting site entitled 'Learn Your Pet Rabbit's Body Language' that you might want to take with a pinch of salt, but still worth a read. Here's a bit:
A rabbit will thump his hind foot in order to warn of danger. If your rabbit is thumping his hand foot, he is trying to tell you that he senses a danger, such as a cat at the door, a noise he doesn't recognize, or it may simply be he is scared of something, and wants to warn you of that danger too. Thumping is a communication tool, so if your bunny is thumping his foot, you can know he loves you and is trying to protect and warn you of the danger he senses.