The Stormcloakes are pretty much Nationalists, either you're a Nord or you're not a Nord; and if you AREN'T a Nord, then GTHO. By starting his rebellion shortly after the Thalmor invasion and current occupation of Skyrim, Ulfric has taken advantage of the political/economic/military situation to make Skyrim a "Nord Only" state that won't adhere to the Thalmor restriction against worshipping Talos. This makes the empire weaker, and puts every other state at risk, (The Thalmor could use Skyrim as a justification for harsher laws and an increased police state.)
The Imperials, on the other hand, are just trying to restore order so not to enflame an already tense situation. If the empire stands united, even under military occupation, then it makes it that much harder for the Thalmor to control the continent.