Stormcloaks are a tad racist but they are not homicidal toward other races. They just feel better than them. This is wrong, but they aren't the ones who are rounding up people for torture and execution for practicing their religion. Thalmor are nazis and the Empire is letting them get away with it. Do they like it? No. Can they stop it? No. But that means the empire has failed and NEEDS to fall. It's time for a change. If other nations see the Nords succeed in taking down the empire and driving out the Thalmor, they will follow their example.
Empires fall but nations endure. It's time for the people to be governed by themselves, not some puppet pulling the strings and having his own pulled in kind.
I was giving the OP my initial reactions... any serious discussion as to the merits and issues with both factions is best dealt with in the Spoiler section.
However, I can address a few non-spoiler arguments. For instance, other nations have already risen up against the Empire. The in-game Lore is rather specific about the Empire being on its last legs. Valenwood was won by the Thalmor via insurrection early on. Argonia also separated due to Thalmor interference, but the lizard-folk didn't fall to their sway either. Elsweyr has joined the Aldmeri Dominion as a pair of client states. Morrowind was almost entirely destroyed by a natural disaster. Hammerfell split with the Empire at the signing of the White-Gold Concordat. Skyrim and High Rock are all that are left of the Empire's non-Cyrodiil provinces. There is no inspiring change that will take place if Skyrim were to join them. Instead it would be a powerful symbol of disunity.
I find the idea that an Empire must fall, and that all the blood shed by its destruction is somehow justified, to be abhorrent. It might be hard to see given how abstract the gameworld is, but people who only wanted to live in peace had their lives ruined because some people decided that this Empire had to die. Not even an attempt at reform, no, but immediately a charge for bloodshed and chaos. That is not a cause I can get behind.
EDIT: Was it just my imagination, or was this is general just a while ago? 24 hours of no sleep is messing with my head.