I would expect that she may stop much of the thumping after she has been around you for a while and is used to you.

Since she is a new bunny to you, I would urge you to spend as much time as you can down on the floor with her. Most bunnies do not like to be picked up because they can't get away, they may even struggle with you and could end up hurting themselves.
Remember rabbits have been prey animals and have therefore been food for others for thousands of years... As a result they are naturally fearful of anything bigger and louder than they are. You have to earn the bunny's trust first, unlike most kittens or puppies who seem to automatically love everybody.

By getting down on the floor you appear much smaller to your bunny and therefore not as threatening to her. Watch Tv, do your homework, read...bunnies are very curious and eventually she'll come over and check you out. Say her name a lot so she gets used to it and the sound of your voice. It depends on the bunny and the amount of time you spend with her but after a few days of this she should see that she has nothing to fear from you.