Specifically, upgrade planet infrastructure (in planet development menu, its the option with the image of a person). Planets need to have their infrastructure upgraded at least twice for their income rates to become positive 100% of the time (asteroids 1, but that's all they support anyway).
Trade ports are also another method of income, their income rate is influenced by your longest chain of trade ports and the number of trade ships (each time a trade ship is destroyed, the income rate of the port that built it drops to reflect the loss of that ship until its rebuilt). Killing enemy trade ships also gives you credits, but that's not practical - just watch out for Advent trade drones with Karmic Retribution.
