User blog comment:Thedoucheinthenorth/The Civil War - Why it is great/@comment-4237253-20121103071141/@comment-3492791-20121103194216

Tullius is simply a military commander. He directs the forces within Skyrim, but his orders come from even higher up. Thus it is generally considered that he is just a pawn in the scheme of things no less than any other "faithless Imperial".

Ulfric on the other hand is the highest ranking person in the Stormcloaks, and is chiefly responsible for initiating the conflict. The entire rebellion rest squarely on his shoulders.

The difference is that the Stormcloaks wish to secede from the Empire, while the Empire wants to quell the rebellion. The Stormcloak plan is to show the Empire that they are to be reckoned with, and to this end kill Tullius as an example and a message. The Empire's plan is to kill Ulfric and stop him from rallying people to his name.