Tallullu - Tabby is right on! Bunnies thump when they feel threatened and when they protest something. For example, I dropped some greens into Jack's pen, and then I realized I hadn't rinsed them, so I took them out. Well he started thumping. He didn't approve of that at all!
So, your bunny thumping is just his way of communicating and it has nothing to do with giving "too much freedom" He may thump just to let you know he's not happy with what is about to happen and that is just part of his personality. So Tabby's idea of enticing with a treat is a great one.
Mine now know the word "treat" and come running into their pen when I say "Treat Treat!"
So when you are giving him a treat - just say the word and soon he'll associate it with that word.