Usually racism in a sprite (in a RPG NPC) is a clue that they're supposed to be the "bad guys". While watching a youtuber do the Stormcloak questline, there are some disturbing hints of racism you see in the progression of the quests. In that way you tend to want to support the Imperials.
I don't know what you mean about disturbing hints in the progression. Personally I think the racism angle is a play on expectations. In one of his posts MK talks about how the "Nords' largesse to their ancient enemies" is one of his favorite things out of the Red Year. And you expect the Nords to be backward and inward looking. On the surface that's what you find, and some people just stop there. But there are all sorts of inversions of the tropes in the details. In Skyrim it's the Stormcloak holds who took in Dunmer refugees and have the most "diverse" populations. The guy on the docks in Windhelm is exploiting his workers, but Bolli in Riften is a convert to Mara and the soul of generosity. The woman being harassed by Rolff and Angrenor will later talk about worthless lizards when you meet her in her office on the docks. And the fact that the Argonians are kept out of Windhelm probably has to do with the fact that they slaughtered their way through southern Morrowind after Vvardenfell, in retaliation for centuries of slavery. A couple of the Stormcloak jarls have more non-Nords in their households than the imperial ones do.
So all these things I see as a bit of trolling on the part of the writers. You're expected to think the Stormcloaks are racists and Nord supremacists, but the truth is much more complex and is in some respects the reverse.