Separatists are a mixed bag when it comes to politics. Any group of people regardless of political belief would consider seceding from a government they viewed as corrupt or unfair. This is a libertarian concept. Any group that wants to leave another group should be allowed to do leave peacefully and form their own society.
In the prequels, the Confederacy of Independent Systems (CIS) gathered a large group of planets sick of the Galactic Republic’s high taxes, bureaucracy, incompetent leadership, and unconstitutional laws. The new alliance of systems, however, was merely a ruse devised by Chancellor Palpatine for gaining emergency powers to become a dictator. Palpatine used controlled opposition to extend the war long enough to destroy the constitution and kill off everyone who disagreed with him and his new Galactic Empire. By the end of the fighting, Palpatine emerged unchallenged as the single most powerful man in the galaxy, with his apprentice Darth Vader. Still, the new Rebel Alliance emerged from the ashes of the Separatists and proved to be an opposing force Palpatine could not control.