This is just from my experience, but when I first started riding, and when some other girls that I know started riding, the two things they were most uncomfortable about were :
1. knowing how and when (and what gear!) to shift and causing a "burden" upon other people when they screw up
2. Falling.
I overcame both of these fears - the first one by practicing in little "playground" areas with a variety of terrain (i.e. sharp turns, mud, hills, flats, etc...). I would actually think about how I was going to shift before I made it to the "obstacle" and then I'd repeat the exercise about a dozen times. It was definitely a "baby steps" method, but it worked... now I am totally comfortable shifting while flying up a hill over rocks, etc... and it is so much more enjoyable when it becomes second nature and you just understand why you need to shift instead of freaking out about it.
The falling thing - I fell the first time I ever went riding, so I got over the fear quickly. One thing I noticed - when I started riding, I would try to go slowly through a tricky section (i.e. mud, or something like that), partially because I was afraid I would fall. Now, I know, that in sections like that, it is SO much easier to just gun it and fly over...I have fallen SO many times now... it is pretty ridiculous, I've had one really bad fall, and I was remarkably OK, and I dislocated my shoulder once, but it never really hurts at all during the fall - only some war wounds afterwards, which look cool anyway. :) Take her riding in some areas that don't have a lot of rocks, and when she has her first fall, believe me, she'll realize it isn't all that bad. My bike lands on me all the time, and as long as I am wearing the proper equipment, I always get right back on.
Speaking of which - does she have proper equipment? Boots make a huge difference in confidence... also, if you want to go the extreme route, which I did, purchase a Dainese body armour suit. Very expensive, but VERY VERY worthwhile. I have a full body armour suit that I wear under my Fox Racing gear, and the pain when I fall is next to nil. Maybe she needs to feel more protected like that and less vulnerable!
Good luck!!!
Stacy