1) She has inherited a shy, retiring temperament, first of all.

2) Perhaps before her arrival at M.P. her Mother gave her strict admonishments on the differences in manners at a landed gentleman's estate and possibly emphasized her "inferior" status in that family.
3) Her cousins were older than her and I never read a hint that she had a peer who she could play with, confide in, and share her feelings. (although Edmund is so kind and caring, he is a male and still older than she is, thus not a peer.)
4) Indeed Mrs Norris was deliberately cruel to young Fanny and reinforced her inferior status at every point.
5) She seems to have never been physically robust or healthy and therefore, her natural energy level is beneath most others, another reason why she is so retiring and quiet....possibly to conserve her lower energy level.