In the sub-genres I have labelled as politically relevant, bigotry can certainly be found, and it does play an important role, just not as clearly defined as you could find it for example in C. J. Cherryh's Faded Suns Trilogy, where mistrust and fear for the other is the driving force behind the entire plot of the series, and the inevitable search for understanding upon which one human being embarks.
It must also be taken into account that when dealing with science fiction race has entirely different meaning, it no longer is about skin color or national origins, it can perfectly be of an entirely different animal family; while we evolved from mammals it is absolutely possible to run across a story in which that "other" is descended from lizards, or insects.
This opens up the stage for the issue of bigotry as a driving force for political and social development. In the universe of Orson Scott Card's Ender series (both the original and the latter Shadows sequels), the starting point is a fight between "us" and "them", the bugs, later known as the Hive Queen.
Now this bigotry can be understood perfectly fine, after all the aliens tried to invade us, and we are just fighting back. But on the Shadow Series, especially in Ender's Shadow, bigotry is taken to a whole new level. Upon the defeat of the Hive Queen in her native world, the children from Battle School are sent back to their countries of origin, and since they are known to be military geniuses, each and every one of them is treated as a national asset by his or her government, and once the external threat has been vanquished, mankind is back to its petty squabbles over skin color and religion, which are only overcome after a brutal and costly war, where the Battle School children are the first casualties, even if they do not die.
Another example is a short story whose title I haven't been able to remember, but in which we see a time traveler going into a ravaged United States, torn apart by war, hatred and famine. The astonishing thing is that this is the result of a racial war between African Americans and Caucasians, where the rift was so wide that no side emerge the victor. And spoiler alert here, the last scene of the story reveals to us that the main character, the time traveler, is a black man. Similar setting as the one in Philip K Dick's Counterclock World, where the continental US has split down racial lines and it has become two countries, one for blacks and the other for whites.
If anyone know the title of the story I'd really appreciate you telling me. I read it a long time ago in an anthology taken from the library in another city, and have not been able to find either the book or the story again. Any other examples of bigotry, not first contact kind of bigotry that is, are also appreciated.
And finally, do you think that only through an external threat to our survival will we be able to overcome racial barriers and stupid hatreds? or will we find a way to reconcile our racial differences some other way?