I had a Great Dane that was just like that. I got Gypsie at three months old, and everyting scared her. The slightest loud noise, too harsh of a tone, too fast of a movement, and she would cower like she was going to be beat. I never struck her or anything. We were always kind with her. When I got her some obedience training, that helped some. It also got better as she got older. She was always a bit jumpy all of her life, but not as bad as when she was a puppy. Hopefully, yours will get better, too. Just remember to have patience.

PS. I talk about Gypsie in the past tense because she died 3 yrs ago at the ripe old age of 12.