Has she been spayed yet? If not that will be a major part of the problem and you'll need to get her done.
Some buns just aren't 'cuddly' anyway. My Pickle hates to be held, even though I've had him 6 years. If I get on the floor with him though he's really friendly. I suppose, putting yourself in their shoes, it is a terrifiying thing to be picked up, and you should therefore limit it as much as you can. If you need to take her anywhere use a carrier, and when spending time with her do it at her level, on her terms. Good luck!