The Doctor is a character who is constantly changing. With every new incarnation of the character, you get a new face, new clothes, and a new personality. But sometimes that personality isn't so good. In fact, for a guy who's all about helping people, there are times the Doctor is a complete jerk. The worst things the Doctor has done aren't very grand, but they're definitely destructive to the people around him. On a bad day, he doesn't go around destroying civilizations: he shatters the lives of everyone he cares about.
Really, the brand of d*ckishness depends on the Doctor. Ten could be righteous and absent-minded, Seven was a Machiavellian schemer, Twelve could be pretty darn insensitive, Eleven was kind of a sociopath, and Six was... well, we'll get to that.
Sure, at the end of the day he saves more people than he hurts, but there are still times examples of the Doctor being a d*ck. Need evidence? Check out these instances of the Doctor being a jerk on Doctor Who and vote up the most messed up things the Doctor has done.