Or to use a fantasy example it's like saying the kids from Chronicles of Narnia are the bad guys for overthrowing the White Witch or that the Rebels in Star Wars are bad for killing Emperor Palpatine and replacing the Empire with the New Republic

Heroes taking down an evil ruler and replacing them with someone who will rule better and more fairly than they did is an age old trope in fiction that has an "Evil empire/villainous monarch" as the foe