The Confederacy of Independent Systems was created by the Sith Lord Darth Sidious under the guise of Chancellor Palpatine and his apprentice Darth Tyranus under the name of Count Dooku, as a reason for the republic to go to war.
Palpatine was granted emergency powers during the conflict allowing him for all intents and purposes to be a dictator.
The war also allowed the Jedi to be stretched and thinned until Order 66 was given effectively ending the Jedi as a threat to the Sith's plans and enabling Palpatine to start the Galactic Empire.
The CIS were nothing more than a tool, and a tool wielded to accomplish an evil purpose cannot by definition be the "good guys".
Once its purpose was finished the tool was discarded, by the new Sith Lord Darth Vader when he killed the CIS leaders on Mustafar. This also would have prevented the CIS from forming an actual independence movement against the newly formed Galactic Empire.
The methods used to manipulate the leaders of the various factions within the CIS were mostly greed, lies or fear based. Nothing altruistic on the part of the leaders. Various systems that joined may have been swayed by Dooku's speeches on removing the evil at the heart of the republic, similar to his speech to Obi-wan but that is conjecture & wouldn't make CIS as a whole good.