The Doctor learns that he is bigoted because he refused to accept the idea that a Dalek could be good. Indeed, he hates Daleks so much that the one time he is prepared to even countenance the idea of a good Dalek is when he meets a Dalek which says all Daleks are evil and should die. So he hates genocidal racists so much that the only member of that race he can think of as good is the one who says that it would be a good idea to exterminate an entire race. But, of course, that isn't good. That's bad. That makes you as bad as a Dalek. Indeed, that's Dalek-thinking.
Ironic, fairly interesting, and doubtless intentional.
But there's another interesting irony here, which probably wasn't intended.
As has been frequently pointed out, SF often falls into the trap of a race essentialism. Alien races in SF all have the same characteristics. The same sort of thing is true in Fantasy, and in other forms of storytelling featuring sapient non-humans. All Vulcans are logical, all Sontarans are militaristic, all House Elves are servile, all Orc are psychopaths, etc. The problems with this are obvious. It rests upon a reductionist view of race, society and sentience... not to mention a set of assumptions directly related to biological racism. But that's all obvious, and well covered elsewhere.
Back to the unintended little irony in 'Into the Dalek'... which, to be fair, is more an irony about the Daleks themselves. No, not the irony of creatures which metaphorically express the evil of racism themselves being based on race essentialism. I'm not really talking about race here. I'm talking about politics.
Because, as is also well understood, the Daleks are metaphors for the Nazis. Actually they hardly even bother being metaphors.
So we wind up in a peculiar situation politcally when we question the idea that there is something wrong with assuming that all Daleks are evil (an assumption that 'Into the Dalek' more or less explicitly questions). We wind up essentialy questioning the idea that all Nazis, all fascists, are bad. But you see... they are. By definition. The DWM review of Timewyrm: Exodus said that Hermann Goering was the closest thing to a nice Nazi (a pretty startling remark if you know anything about the man). But you can't have nice Nazis. You can't even approach that. It's like talking about dry water - if it's dry, it ain't water.
We have bumped up against a standard misunderstanding about discrimination. It isn't something that can happen to anyone or everyone. There's no such thing as 'reverse racism', or 'misandry' (at least as the term is meant by the crybabies who object to feminism on the basis of their bruised manfeels). There certainly isn't any such thing as unfair discrimination against fascists. That's why they shouldn't be allowed on Question Time, no matter how many people vote for them. You can't have democratic fascists. Obviously, therefore, you can't extend them the boons of democracy. I'm not in favour of banning fascist parties or imprisoning fascists - because it would be counter-productive - but it isn't an unreasonable idea in itself.
(Similarly, I don't think its an unreasonable idea in itself for capitalist democracy to lock me away too, since I've repeatedly voiced my desire to see it destroyed... though it makes considerably less sense than locking fascists away, since my dissatisfaction with capitalist democracy is based on a rejection of its own rhetoric about democracy, and a demand for more democracy, whereas the fascist objection to capitalist democracy is based on a desire for less democracy.)
My saying that it is right to discriminate against fascists certainly doesn't make me as bad as a fascist. That's wishy-washy, purblind piffle. That idea rests on a false equivalency, like many liberal cul-de-sacs. The eternal phantasm of the level playing field, the balanced middle-ground; the idea of the centre as the rational point between irrational extremes, and fairness as the equidistant zone between claims. All that childish, politcally-illiterate shit.
You don't become a fascist when you discriminate against fascists; you become an anti-fascist... just as you don't become a sexist when you challenge patriarchy, or a reverse racist when you challenge white privilege.
Of course, it might be objected that you can label everyone who ascribes to a political philosophy 'bad' without accepting that it would be a good thing if they were all killed... and you'd have a point. But it's still interesting that, even today, we are more comfortable playing around (albeit questioningly) with the reading of the Daleks which is based on race essentialism than on the reading which is based on political philosophy... even when they openly represent a political philosophy that 'we' supposedly all despise.