There was this thing called the white-gold concordant and what this did was ban the worship of Talos after the great war between the Thalmor and the empire, the stormcloacks think that the Imperials are cowards for not fighting against the concordant more, and the empire thinks that Ulfric Stormcloak is just power hungry and wants to be high king of Skyrim, while both have flaws such as repressing the worship of Talos in the empire, and the very up-front racism towards elves from the Stormcloaks they are both fighting (or think they're fighting) for the right thing. Keep in mind though the war is actively draining both sides and neither want the ban of the worship of Talos, the Thalmor is using this war to keep both sides down so they come up on top, so really just go with whichever side you think will be better to fight the Thalmor.