I have a dobie for the first time, a 3 1/2 month old rust/red boy named Chewbacca, "Chewie". He is already dog aggressive and shys away from people, so I am hoping sooner than later his breeding will start taking over and he will become more possessive of us and the house.
Welcome, I would just like to add a little something.
At 3.5 months old he is not confident and "protective" if he shys away from people at this age. That is NOT a good sign for a young puppy, also dog aggression that young is also a very bad thing.
That is not a safe dog to have around your house, esp. as he grows older, and cannot even be around to protect when people come over, as you will have to put him away b/c he is so shy and aggressive. It isn't something I would encourage.
As someone else has said, a shy nervy spooky untrusting baby puppy is not a stable confident protector. He is scared of things and to be a good protector like the Dobe should be, they should be socialized and confident of new people and places - esp. at such a young age, that worries me. Dog aggression in a baby puppy is cause to be concerned. You are right, that probably is his breeding as well as a bit of how he has been raised. Maybe a bit of his disability too.
Possiveness is not good, protectiveness is. But at this young age, he is not being protective, those instincts don't kick in until older, and right now he doesn't have the experience or maturity to understand what is a threat and what isn't, esp. based on what you described.
Sounds like most everything is a threat to him, other dogs, and people, which you will want to work on correcting immediately with LOTS of socialization and dog training classes with professionals and experts within the working breeds. Do you know what socialization is? That is taking them as many places as possible, car trips, errands, oil changes, friend's homes, family's homes, walking trails, lakes, camping, kid's games, the vet (just for treats and weighing if you don't have any real reason), dog food places, and basically as many places as possible and let him know people are nice, let them give him special treats and get to know him a little bit.
Personally, my dogs are very protective, and I feel safe b/c I can take them anywhere and everywhere and have them out when people are over b/c they are stable and confident and know a REAL threat vs. petty stuff. They watch, rather than react right away, they assess the situation.
The Doberman temperament actually faults shyness big time, or overly aggressive behavior. The correct Dobe temperament is confident, stable, alert, fearless, watchful, loyal, determined, and obedient.
I don't mean this in a bad way, I just want you to know, in case you don't, so your dog and any other Dobes you get grow up to be reliable, confident, and aren't overly reactive.