If she was sitting near the window, chances are she saw or heard something outside which scared her. It doesn't take much. As prey animals, rabbits are very easily spooked, and while their eyesight is very good in terms of low-light sensitivity and coverage - they can see nearly 360 degrees around them - it isn't very sharp. It's possible that a bird few over, or something ran nearby, and she saw that as a threat. Their hearing is incredibly acute, so it's also possible that she heard something which scared her - a dog barking or a coyote howling, or just some noise in the house she didn't recognize.
Natasha Rabbitova will occasionally run into my room in the middle of the night and thump until I wake up and tell her everything's all right. Sometimes I have to get out of bed and go look, and that will satisfy her. Once or twice I didn't react quickly enough and she jumped up onto the bed and thumped next to my pillow - that will wake you up right away, no matter how sound a sleeper you might be. A few pets and some reassuring talk, and she was ready to hop off and go back to sleep.
Just talk to her calmly and reassure her that everything's OK. Maybe you can entice her out from under the bed with a favorite treat. She'll calm down eventually.
