A colony's surplus is bottom line of its income from taxes and expenses. Some income may also be generated through food sales. The wages you pay for workers and storage rent factor into the cost side. Non-colony specific running costs, i.e. ship upkeep, blueprint storage or empire tax do not factor into this metric.

Colony stats give you some insight into its economic welfare and where money comes from and goes to. Efforts to improve the private economy are well worth it, as they reduce the impact of taxes and permit you to extract more credits.