They've been segregated in one part of that city for two centuries?
I believe (don't quote me on this) it happened gradually, and the oppression and squalor that's set in only really happened under Ulfric's reign. His father, Hoag, was supposedly much kinder and more welcoming to the Dunmer (see: "Scourge of the Gray Quarter"). I think what Raestloz meant was that Dunmer have been living in Windhelm for far longer than Ulfric's been alive, which is true.
(Actually, as for the Gray Quarter itself...I suspect the sudden influx of a bunch of refugees from the Red Year had more of a hand in the segregation than Ulfric did. Refugees tend to stick together rather than disperse throughout a city, so the Dunmer migrating from Morrowind--at least initially--probably kept mainly to themselves. The problem crops up when, 200 years on, they're all
still keeping to themselves and the Gray Quarter's turned into a proper slum under Ulfric's rule. Basically the segregation was there from the start, the trouble is Ulfric's content to keep it that way and just act as if the Dunmer in his city aren't his problem.)
Of course, it's a two way street--go read the book "Dunmer of Skyrim" sometime. There's some Dunmer who are just as racist against the Nords. The two races have been bitter enemies for a very long time prior to the eruption of Red Mountain; I believe the Nords even invaded northern Morrowind as recently as during or just after the Oblivion Crisis. There's more to this story than just "Ulfric Stormcloak is a racist facist."
As for "
all Stormcloaks are racists"...meh. Blanket statement is a blanket statement. There's clearly some more accepting folks who ally with the Stormcloaks. Ralof and his family for one--they'll take you in regardless of your race. Wuunferth and Jorleif seem like decent folk, too.
...But then you've got folks like Galmar Stone-Fist (who's a jerk no matter what your race, but he goes out of his way to insult you if you're a Khajiit, for instance) and his relative Rolff Stone-Fist, who's the drunk that goes around harassing the Gray Quarter. They have the same last name, so I assume they're related anyway.