First, a history lesson:
The Great War was a war between the Thalmor and the Empire about 30 years before the game begins. The Thalmor is the Altmer, totalitarian, elitist and fascist head of body in the Aldmeri Dominion - another Empire that encompasses the Summerset Isles, Valenwood and Elsweyr; the homes of the Altmer, Bosmer and Khajiit respectively. They came to power after the Oblvion Crisis when the Septim Dynasty fell and the Daedra were driven back by Martin Septim and the Champion of Cyrodiil. The Thalmor however, claimed that it were them that rid Tamriel of the Daedra, and thus were revered by the majority of the Altmer populace, and were inaugurated as the leaders of the newly established Aldmeri Dominion. Altmer dissidents were hunted down and killed, and a 150 years later, when the provinces of Elsweyr, Black Marsh and the newly occupied by the Argonians, Morrowind, left the Empire, the Thalmor attacked the Empire with swift and unmerciful wrath.
The Empire, which had it's hands full with striking down insurgent rebellions, were completely surprised by this, and the Thalmor devasted the Empire, sacking the Imperial City. A year after the occupation of the Imperial City, the Empire struck back, claimed the Imperical City once more and wiped out the Thalmor army in Cyrodiil completely in a great battle called "The Battle Of The Red Ring".
However, it was not without loss and the soldiers were all tired from the years of fighting. The Empire was forced to sign a peace treaty with the Aldmeri Dominion which was heavily in the Thalmor's favour. The Empire gave up a part of Hammerfell and agreed to ban the worship of Talos. However, the Redgaurds didn't take too kindly on giving up a part of their homeland, and they seceeded from the Empire aswell, leaving Cyrodiil, High Rock and Skyrim to be the only remaining provinces of the Empire, however with Morrowind's Dunmer populace still supporting them. This secession eventually let to the Aldmeri Dominion attacking Hammerfell, but the Thalmor was driven back by the Redguards single-handedly.
A short time after the Great War, the native people of the Reach attacked Markarth and claimed it for themselves, once more after it had originally been conquered by the Nords. Ulfric Stormcloak, then a legionary of the Empire, made a deal with Jarl Igmund of the Reach: If Ulfric and his legionarys would help take back the Reach, they would be free to worship Talos, also known as Tiber Septim, an ancient Nord who founded the Empire and the Septim Dynasty and then acended to divinity. Jarl Igmund agreed, and Ulfric claimed the Reach for the Nords once again, and were free to worship Talos. However, the Thalmor found out and began dragging people off in the night and killing Talos worshippers.
Then Ulfric founded a small personal army to forward his ambitions, which later got the name The Stormcloaks. He felt that the Empire had failed him by signing the "White-Gold Concordat" (the peace treaty that ended the Great War) and thus began to speak out against the Empire and for an independant Skyrim. He didn't get much attention by anyone, but after he killed the High King Torygg of Skyrim, a man who stood up for the Empire, he suddenly recieved everyone's attention - including the Empire's.
The Rebellion and Civil War has now been going on for about 6 months, and HERE WE ARE! Caught in the ambush by Imperial General Tullius, Ulfric manages to escape... And you must decide the rest of the income.
Now here's my point of view:
The Empire had no choice but to sign the peace treaty - fact. The Empire is the only thing that stands between the Aldmeri Dominion and Skyrim - fact. If Skyrim became indepedant, it would be VERY costly, and the Thalmor would see a golden opportunity to attack Skyrim and make it a part of the Aldmeri Dominion. The Thalmor has grown in strength since 30 years before, so there is not a chance in hell that Skyrim could stand up to the Thalmor like the Redguards did - remember they battled the Thalmor just after the debilitating Great War - to think that the Nords would also be able to drive the Thalmor back after a civil war is preposterous! The Empire have already shown that they can stand up to the Thalmor, even after such a large-scale surprise attack - the Empire will, as soon as they feel that they are ready, break the peace treaty and allow worship of Talos once more. The Aldmeri Dominion will do whatever it takes to convince you, that they have the upper hand, but that's crap. The Empire is growing strength, but if they lose Skyrim, they will probably lose the next great war aswell and thus allowing complete domination over Tamriel by the the elitist and fascist Aldmeri Dominion. A united Empire is better for everyone.
For good or ill, the Empire is the lesser of two evils - and that is only so, because of the ban of Talos worship.
Really? Those are facts, huh? Please don't state that because it ends up making you look like a [censored].
"The Empire had no choice but to sign the peace treaty - fact."
They had as much of a choice as they did to agree to the very same terms that were offered to them before the war started. What 'forced' them to accept the treaty? The fact that they had annihilated the Dominion's entire Cyrodiil Invasion force, while still having half of their Leigons intact? The fact that five years after the signing of the WGC, the Hammerfell invasion force didn't have enough resources to continue fighting the independant Redguards, whom their whole army was stuck in a stalemate with?
"The Thalmor has grown in strength since 30 years before, so there is not a chance in hell that Skyrim could stand up to the Thalmor like the Redguards did..."
So has the Empire and the other human provinces. And remember, Men reproduce at a much faster rate than Elves do. And Skyrim would have a large amount of combat-ready soldiers, because it was not touched during the great war, the only Nord casualties were the Nords that served in the Leigon. Yes, the Nords, who make up the Leigon's finest warriors, rivaling the Redguards. I wonder how much of a chance the Aldmeri Dominion would have in invading the homeland of the Nords and defeating them.
Ulfric did not make a deal with Jarl Igmund. Jarl Igmund pleaded with Ulfric and his militia, he is the one who made the offer to allow them free worship of Talos.
And why would Skyrim's Independance mean that the Thalmor will attack? If they were ready to attack, they would've destroyed the Empire already. If the Thalmor stood a chance against the Empire after Red Ring, they wouldn't have agreed to the peace treaty. They would've continued waging their war against the Empire because the eradication of men is one of their ultimate goals. Unfortunately, the profound general but poor politician, Titus Mede II, greatly over-estimated the Dominion.