Anybody who supports the Stormcloaks is a terrorist. A racist, Thalmor-loving terrorist.
The Imperials wanted to execute me, just because they found me in the wrong place. That doesn't make me want to side with them.
Yeah, but I can't really think of a circumstance where they're a greater evil than the Stormcloaks, a sect of xenophobic patsies for the Thalmor, who quite frankly are the real enemy here. Even a Stormcloak victory would soon enough be a Stormcloak defeat once the Thalmor dismembered the Empire. At least united there's a chance to stand against the elves, even if the Empire lost the last war.
That's assuming the Dragonborn isn't alive by that time and would just sit on his ass should that happen. Seriously, he has the power to incinerate an entire detachment of troops with a mere utterance, he can send heavily-armored troops flying into mountainsides and trees with just a few words, let's not forget the absolutely absurd amount of combat experience he's accrued by this point, and is likely decked out in armor that absorbs all but the strongest of blows, and quite possibly has spells that can end entire armies. And let's not forget that its entirely within the realm of possibility that he's the richest motherfucker in all of Skyrim, if not the whole of Tamriel, so he could easily pay for an army of his own...or just buy enough potions to keep him going through days of Thalmoor slaughter.
The Dragonborn basically becomes fucking Jesus by the end of the game. The only conceivable way for the Thalmoor to win would be to wait until the Dragonborn dies of old age, which, if he's an Elf, is going to be a long. Fucking. Time. And all this, all this, is assuming the Dragonborn doesn't just go on a crusade against them and wipe them off the face of Nirn. Remember, people practically fucking worship the Dragonborn; he could literally go Christ-figure on Tamriel and lead a holy war with casual ease.
The motherfucker basically killed Satan. The Thalmoor don't stand a chance in hell. No one does.
[ETA]
Oh, and let's not forget he's also probably done favors for most, if not all, of the daedra lords, which are tantamount to gods. Azura, one of the chief members among that enclave also has a sense of fair play, and is generally on the side of good, or is at least portrayed as such. Azura, the same fucker who
turned the skin of the Dunmer dark and made a volcano explode because she was pissed. Yeah...go after someone whom she owes a favor.
Smart idea.