Do you know the rabbit's age?
The first couple of day, rabbits are usually highly stressed. It is actually best to leave them alone in their cage for the first 48 hours undisturbed. Since that didn't happen, I'd suggest doing a "do-over". Just leave her alone in the cage for 2-3 days (aside from refreshing food/water). Give her time to adjust to her new surroundings. There is quite a bit for a bunny to get used to in a new home. All the smells, sights, and sounds are new and different. Just go about your usual business so she can get used to the usual sounds and routines.
The growling and thumping could very well be hormonal (as whiskey suggested) or it could be (or also be) because she is still adjusting to a new place. A rabbit can growl and thump if feeling threatened (from her perspective) or just scared. The fact of that cage door being open can itself be a frightening thing because it takes away her secure feeling inside the cage. That's why it would be a good idea to just shut her in for a couple days and let her get adjusted in the "safety" of her cage.
Once you've done that, just open the cage door and back away. Allow her to come out on her own if she feels up to it. Some rabbits will be ready to explore, others will proceed slowly and cautiously- ever ready to hop back into the security of their cage. Just let her proceed at her own pace (once you've confined her for a couple days).
