No, the Stormcloaks are not like the Nazis.
A few points I think prove that:
They do not seek to expand beyond their homeland and enslave the world under the Nords, they only want to liberate their homeland.
They are not after ethnic cleansing(where do people get that idea? I find no evidense for it in the game)
Windhelm is the only city with so called segregation, but that is only because that part of the city was given to the Dunmer almost 200 years ago IIRC.
Sure, they are nationalistic and pro-nord, but Nazis? No, the Thalmor have some similarities to the Nazis, but neither the Empire or the Stormcloaks do.
I just want to add that sure, they have a couple of idiots like Rolff Stone-Fist among their supporters, but in general, they aren't any worse than most other Nords. Than most other races, in fact. Most races in Tamriel seem to be pretty racist against the others, Dunmer and Altmer being far worse than Nords, IMO.