Aw, poor baby. Lots of puppies dont like people walking straight up to them and petting them on top of the the head, i think it's kind of threatening to them. Try to have people come up to her and pet her side while you give her praise or treasts for being a good girl. As much as you want to, try not to coddle her for being scared, just act like there is nothign to be scared of. On the flip side, dont force her into any situation that she seems scared of - let her do it at her own pace. Use treats to your advantage, find somethign that she really likes and offer her rewards for doing the things that she seems scared of doing.