User blog comment:Thedoucheinthenorth/A question of morality/@comment-1600847-20121209142434/@comment-1600847-20121212041048

Whiterun is not neutral. If you side with the Stormcloaks, Whiterun sides with the Empire. If you side with the Empire, Whiterun sides with the Empire. Either way, it supports the Empire.

But you're right, just because the city does support one side doesn't mean the people do. Just like the Stormcloak cities have people who do not support Ulfric at all, a lot of Imperial cities have people who don't support the Empire.