How do I make my new rabbit feel comfortable?

Make sure she's in a quiet room with just you, set up the room to make it "Rabbit Friendly", make sure she can't hide anywhere or choke on something. Let her explore her surroundings, for a few minutes a day, and add on to the time you allow her to explore everyday(only by a minute or two) Sit somewhere within her proximity, and hold a treat or something each time, eventually she will warm up to you and take it from you. She just needs some time. I recently got a hamster and he was extremely nervous, he's still rather jumpy. He has become more comfortable though. Just ease into it rather than force it. Let the bond come naturally. Hope that helps make your little bubbers feel better! :3