The Cyborgs were communists. Humans created the Cyborgs and then they rebelled as communists. Humanity canonically won the war against them in the first game and now the Cyborgs are imprisoned on a mining planet called Cyberstan.

The Automatons were created by the Cyborgs and hold the same ideology. At least that's what we're told, I see no reason to believe otherwise.

The current theory going is that the Automatons are fighting towards Cyberstan to free the Cyborgs, who will then presumably join them as part of the faction.