The people with read spots are Snilu's chosen people. Only they can become priests. Also, because the holy scripture says that "all knowledge of the nature of the world must come from Snilu, or it will be impure", the priesthood has a monopoly on scientific research. The people with yellow spots mostly follow the religion of Snilu, or one of the offshoots, such as those that worship one of his mates or offspring. As such, they tend to have more rights under the law. They can even own starships, though the only ones that they get new are cargo ships and mining ships.
The Blue Spots traditionally live with much less advanced tech (think modern day tech) because they don't follow the religion of Snilu or any of its offshoots. Their religion (those that have a religion) are more Eastern in their structure, believing that intelligent life has the potential to meet or surpass the gods. Because of religious persecution many of them have started a rebellion along with many sympathetic yellow-spots and a few red-spots.
There was at one point a race of green-spots, but, due to a holy war between them and the red-spots (they worshiped Snilu's younger brother, who the red-spots believe lost a contest against Snilu, then cheated his way out of payment), they are now believed to be extinct.