Not to belabour this but... I'd argue that there's a big difference between thinking differently because of someone because of some category they were born into... as opposed to something that they have consciously as an adult decided to accept as true or false.
If I were to think differently of a person because of the religion their parents were, say, or the religion that their ethnicty was associated with... yes, by all means, that would be bigotry as much as sexism or rascism or homophobia or whatever. Absolutely wrong.
But to think differently of someone because... oh... they have decided they are a Yankees fan and that way of enjoying sports that they've chosen is anti-thetical to how I believe one enjoys sports.
To think differently of someone because they believe as a consenting and conscious adult that... oh... they agreed with Hitler on a lot of things, it's just that he went about things the wrong way.
Because they voted for Ralph Nader, say, and I think them naive and accidentally doing more harm than good by taking away support from people who might not do as much good as quickly but could actually get elected to government, perhaps
To think differently of someone because they say that by swinging my arm, I have injured their friend Harvey, a six-foot-tall invisible rabbit and I need to go to jail for not believing in this rabbit and for breaking his two front teeth.
It's very very very different from bigotry.
It's not a uniformly positive way of thinking or reacting, certainly, but it's quite different from bigotry.
There is a difference between what we are born as and born into... and what we decide to believe as rational independent adults... the accusation of bigotry, I'd have to say only applies to that first set.