One of my younger cats was like this when I first got her. She had a very rough first few months of her life at a shelter & a hoarder's house that must not have treated her very well
When I first got her from the shelter, she was very jumpy, and if she was on the floor you couldn't get near her to pet her. If she was up high then she loved the contact and pets though, and would start rolling around to get some belly pets. If I sat next to her on the couch I'd have to move very slow or she'd run off. Even if I did move slow she'd always be looking up at me like she wasn't sure what I was going to do.
My parents had a kitten that was from a feral colony that was the same way. She was very jumpy initially, and even if she was up high, she'd still run off if someone walked over to her too quickly.
My parent's cat has really warmed up to people though with all of the good human contact she's gotten. You can now bend over to pet her while she's on the floor, sit next to her, and she's just like the rest of the cats in their house now. Mine has come along nicely too.
The more good human contact your cat gets, the better
If she's freaked out by people over top of her, try sitting on the floor in a room where she's at, and maybe have a cat toy with you to try to get her to come over and play by you. Chances are the toy will be too much to resist and the kitten will have to come over and smack it around a bit.
How old is the kitten?