Well here's why the Stormcloaks are bad:
1) Ulfric murdered the King of Skyrim, when he could have done things more diplomatically. Nuff said there.
2) The entire town of Windhelm is full of xenophobic nords, of which Ulfric is one. I'm an Argonian player mainly, so that is self explanatory.
3) Ulfric was the one who got the Aldermeri Dominion into Skyrim. The Empire tried their best to keep them out.