The Doctor sees himself as a peacemaker, yet he collects enemies like other people collect stamps, or coins, or little glass animals. It’s not intentional, but being a righter of wrongs, a fixer of timelines, it’s inevitable that some beings, or even entire races, are going to get a little peeved with him for spoiling their fun. Humanity isn’t the only race that’s good at holding grudges. For instance, Daleks have very long memories and they really don’t appreciate the Doctor’s attempts to wipe them out.
He has more enemies than any other single being in the history of the universe, though it’s probably not a record anyone else is eager to surpass. From Autons to Zygons, sometimes it seems like half the universe is out for his blood; small wonder that no matter where he goes in time or space, he just can’t seem to keep out of trouble. Even when he’s not looking for it, he tends to fall headlong into it. As talents go, that’s about on a par with being able to stick both your feet in your mouth at the same time, in terms of desirability.
It’s a good thing he enjoys running so much.