Your main source of income is taxes from colonists and natives. Using the HQ tax settings screen you can set your universal tax rates.

A second source of income is from your cities. Your normal cities produce 100mc a turn each and under cities produce 70mc a turn. The big drawback to having many cities is their impact on the growth rate of your colonists and their use of food. If you have too many cites the birth rate will drop to zero and you could run out of food. Each city requires 100,000 colonists and two units food a turn to stay active. If you run out of food or your colonist's happiness level drops to below 30 the cities will stop producing money.

The third source of income is from selling contraband. You will find contraband laying about on many planets. You can also buy contraband and hope for the price of it to increase.

Some races have other gimmicks in making money, such as stealing, prisoners, and ship devices.

You could also trade or sell things with other players in the game. There is no guarantee that the exchange will complete, and you might want to think twice when giving a race a ship with special abilities that they normally don't have.