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When the Doctor saves planets, people call him a hero, but he replies by saying he's not a hero. Like this one time:
I'm not a hero. I really am just a mad man in a box
and this other time:
ROBIN:You are her hero,
DOCTOR: I'm not a hero.
Why doesn't the Doctor consider himself a hero? He is: he saves planets and defeats monsters.
Warning: May contain spoilers. (Mainly from the rebooted series.)
From an external perspective he is typically considered to be either a hero or anti-hero depending on the incarnation and which acts one is considering.
The Doctor himself considers himself to not be a hero for many reasons.
Firstly because he (almost) never seeks situations which would put him in a position to perform heroic acts. Contrast this to 'traditional' heroes who often make it their job to be heroic, for example warriors such as Heracles and Achilles, or more 'everyday heroes' such as firefighters, police and (ironically) doctors. Instead, the Doctor simply travels and trouble usually finds him.
During his travels, the Doctor committed a great many crimes and morally questionable acts, many of which we still don't know the full extent of (e.g. the events of the time war). Aside from the numerous murders he's committed, he's been a guilty party in a number of genocides:
Some miscellaneous examples of the many (albeit less serious) crimes has committed over the years:
On top of which he certainly has a mean streak.
The Doctor remembers the times he's done wrong and the times he's saved lives, and he knows that he doesn't do the things he does to be heroic. He's just a time traveller trying to help out where he can, and he doesn't always get it right.
I dare say if he had the choice he would rather the majority of his trips featured as little peril as possible, like the space tourist he longs to be. Being able to visit a nice hotel without its architect going mad and its inhabitants turning on each other; being able to take a ride on the last ship out of earth without ending up in a whale's mouth; being able to take a trip to a planet made of diamond without encountering a strange mimicking entity; and being able to go to a space theme park without it being overrun by cybermen. Like how Sherlock Holmes retired and took up bee keeping or how Winston Churchill loved to tend to his garden. This was very much alluded to when the Doctor became Victorian teacher John Smith, before being forced to give it up to resume his true persona since he was the only one with the knowledge to save everyone. (The Family Of Blood)
Finally, he's hardly first person to be heroic and then vehemently protest that they are not a hero. Many veterans of various wars have refused to accept their medals because they believed they were just doing their duty, no matter how important what they achieved was or how deserved the accolade might be. There are also various literary characters who have similar feelings about their perceived heroism.
It varies. Sometimes it is because he views himself as ordinary; sometimes because he views himself as a bad person.
The Doctor believes himself to have killed all the Dalek and Time Lords. While one could argue that the Daleks had it coming to them, the Time Lords may not have. In any case, the destruction of an entire species, even a wholly evil and xenophobic one, is nothing to take lightly.
He also destroyed all the young of the Racnoss, and wiped out countless other species. Often in self-defense, yes, and often to save countless more, but nonetheless.
He left Rose in an alternate reality.
He wiped Donna's memories (albeit to save her).
He has caused the deaths of some of his companions (Peri, Clara, Kamelion, Adric), and caused others to be changed beyond recognition (Jack, Donna), or stranded far from home (Amy, Rory, Rose).
This is enough to make anyone believe that they aren't a hero, even if they have done just as many things to help others.
"I am not a good man! I'm not a bad man. I'm not a hero. I'm definitely not a president, and no, I'm not an officer. You know who I am? I… am… an idiot! With a box and a screwdriver. Passing through. Helping out. Learning. I don't need an army. I never have. Because I've got them, always them, because love is not an emotion. Love is a promise."
Death in Heaven [8.12]
He believes (at this point, anyway), that he is no better than other any person.
True, he is a Time Lord, and possesses talents beyond most other creatures in the universe. But then, so does a human, at least relative our current reference pool! Yet we do not wake up every morning feeling like extraordinary sentient beings. The Doctor has plenty of individuals relative to which he can feel inadequate.
Because he is not a hero, he is a Doctor - which needs a bit of Hero in him, of course, but is not a Hero per se.
In The Day of the Doctor, towards the end when the three doctors are looking at the switch that will blow up Gallifrey, Matt Smith looks at Clara and doesn't know what to do.
She reminds him that he has been a Warrior (John Hurt) and a Hero (David Tennant), but what the world actually needs is him: a Doctor. A doctor doesn't save lives for the sake of being a Hero; a doctor saves lives because that's what a doctor does.
Metaphorically, she's describing each of those predecessors as really a part of himself - an element of his character. Doctors must be heroic (by saving the lives of those around them), and warriors (fighting to save those lives). But they also are more than just that - they make life or death decisions intelligently, sometimes choosing something that is not necessarily obviously "right".
Saving lives is what the Doctor does, after all - when he steps in and stops various plots from occurring, it's always for the purpose of saving lives. He doesn't act as a Hero, looking for a bad guy to vanquish, and always Doing Good; he acts as a Doctor, looking for lives to save, and how to save the most lives - even at the cost of doing perhaps-bad things.
I feel that this is often a major part of the character development for each doctor, coming to grip with the fact that he is not a Hero, and that trying to be one often gets him into trouble. Realizing that he has limitations, but that he's also a sum greater than his parts, is how he becomes the Doctor in truth - and lets him make the decisions he must make in order to save the world.
