Not so much with dobies, but your typical large, "aggressive", dog breed owner (I.e. pits, rotties, etc) is not usually the most responsible of dog owners, which is why I believe they have the bad rep. These breeds were created for guarding, protection, gameness for fighting and are VERY strong. They are also strong willed dogs who have a bred in aggressive tendency, if your dog is guarding something, he's not supposed to go up to the intruder and say "Hi, my name is Rover! The silver is this way". Its just their nature. Thus they need a very firm hand and LOTS of training to ensure their behavior will not get out of control because they can and do become dangerous.
Speaking from having had an Am. Staff (smaller pit bull) who we adopted from a stupid teenage boy who did not train him, did not neuter him, and (surprise surprise!) could not control him, I hate to say it but the reputation is there because of irresponsible ownership.
People who do not train these breeds properly are ASKING for trouble. And lets face it, who "usually" owns these breeds? Young males age 16-25 who want a "tough dog", and who have the "if I keep my balls, he keeps his" attitude. BAD BAD BAD IDEA!
Ugh....
To make a long comment short, the "dangerous breeds" may be inherently more aggressive than other breeds because we made them that way. But it's the irresponsible owners that are the real problem, not the dogs. With proper training, any dog can be good.