It sounds like your pup is in dire need of some major socialization. Young dane puppies should be outgoing, into everything, playing non stop, and curious about their new surroundings. There is an adjustment period that usually lasts anywhere from a day to a week with a new puppy coming into a new home, but after the end of that time, the puppy should not be intimidated by their surroundings in their own home.
Who did you buy your puppy from if you don't mind me asking?
Both parents should have allowed you to pet them. The bitch may have understandably been nervous or protective if you were around her and her young puppies, but the sire should have been outgoing, calm, and friendly, as they do not have the "hormonal and instinctive" tendancies to feel the need to protect their young. There are some bitches that will act completely different while their puppies are around, rather than othertimes when she hasn't had a litter.
Are both parents finished with appropriate health tests? (cardiac, hip, eye and thyroid) and have their CHIC numbers? Has the breeder been in the breed, actively showing in conformation or obedience or another sport for several years? Or is it a breeder who doesn't show yet produces "show quality" puppies.
You need to work on confidence building with this puppy, and also get a hand on what may be a dominant pup. Early signs of mounting or "humping" other dogs can indicate a more dominant or alpha dog or bitch. Do not allow your dog to show this type of behavior towards the other dogs (or people) in your home. You don't need to use any kind of harsh treatment with him, just be firm and consistant.
Find yourself a puppy kindergarten class, and get him enrolled NOW. Take him everywhere with you even if you let him sit in the car, so he can see people coming and going. Many dane breeders feel the need to recluse their puppies during the younger states of growth, as dane puppies of some lines can have weak immune systems.. BUT, if you are intending to show this dog, you need to get him out there and get him socialized ASAP.
Temperment is a combination of hereditary and environmental influences, but if both parents showed a marked level of fear or agression, you can almost expect to have a dog of the same mannerism. It could be that this breeder is doing everything right, and that their dogs were showing a tendancy towards feeling the need to protect their home. This IS a working breed, and some lines do show a marked tendancy to protect their homes... BUT, your puppy should not be fearful as you mentioned.
There are a lot of variables about this situation, and a lot of reasons why the sire and dam may have acted this way towards you, but your puppy should not be exhibiting the traits you are speaking of and these are problems that need to be dealt with now, not when the dog is 6 months old, 100lbs, and at that point much more difficult to control and train.
Caroline Smith
FarView Great Danes