There are 5 ways to make money.
Commercial: The most viable way for Terrans and Virals to make their money. Is unaffected by planet type, you will just want planets with the most land possible. Researching Commercial allows you to make more money from commercial buildings.
Tax: By building housing on your planets, you can generate tax income from the population. Downsides include having to feed the population, and waiting for the population to grow. Also, Population increase your PR level (1 PR / 10 pop I think) so you would need more fleet to protect it. Loyalty increases the amount of tax gained from your planets. U.Eden`s, Clusters, and Balanced planets are all good for population as they allow faster growth. Researching Housing increases the amount of pop 1 housing can hold.
Industry: Industry takes raw materials and turns them into Consumer Goods which can be sold on the market or eaten by your population. Population has a certain amount of Consumer Goods demand (dependent on race) and you can feed these goods to them for $5 each. If you make a surplus, you can sell the goods on the market for $4 each. The best race for making goods is the A.Miners
Agriculture: Assigning land to agriculture increases your food production / turn. Food is used to feed your population, and food production also creates raw materials as a byproduct. The best planets for this are U.Fertile and forests. You can sell food on the market. The best races for food production are terrans and collectives.
Mining: Probably the most lucrative of all income types. Each planet has a certain mineral type. Every turn you use, you gain this mineral automatically from your planets. These minerals can be used to build ships are to be sold on the market Mineral production is increased by research mining. Also, planets may have Ore on them. Ore is used for building things on your planets, and can be in heavy demand for some races. You mine ore from planets by assigning mines to them