Miss Hoppy will thump when she is angry, or when she is signally "No!" Zippykat can vouch for that behavior in her previous bunny, Miss Sophie!

So it is quite possible that she is saying "No! I don't like being in that cage! Thank goodness I'm out!"

Bunnies thump to warn you of danger, or in anger, or to say "I don't like that!" A double thump seems to always mean "danger," but a single thump is often "I'm mad!"