I have bad suspicions that your pup was trained to be non-agressive by a woman trainer. She could have been adopted by family with children, and I have heard about cruelty to puppies trained either by breeders, or those who bought them to train in order to resell already trained. I have no idea, what they can do to puppies, but young dogs are scared to walk not any stairs, but stairs of the house, not afraid to ride elevators, but scared to go into the car boot, not scared of big bulky and loud men, but scared of seemingly gentle, short and slim...It cannot possibly be genetic.
I'd advice you to pay attention to the sound of your voice first of all, whether you are talking to your pup, or to your husband. Make it sweet. It can help, if you, together with your husband, take your puppy into your bed with you for 30 minutes before you crate her, let your husband to lift her. Play a game with her normally played with kittens - a feather on a thick woolen thread in sitting position. Smell for her nicely, rub your ankles and forearms with Essential oils for dogs | Essential Animals
. I don't want to give you the same advices as other members of this Forum already gave you. It will take time for her to gain courage.