Simple poll. If your favorite race was rebelling, would you side with the rebels or the Empire supporters? If your favorite race is Imperial, imagine it was the redguards or Nords who were the head of the empire, signed the wgc and got rid of akatosh or Talos worship, whatever, and its basically the exact same situation. For other races like the Dunmer, imagine one of their important gods being outlawed. Like Malacath for Orcs, or one of the tribunal for Dunmer.
I left Nords out on purpose. Same situation, same type of leader, and everything.