First of all, no city ever loses money. The figure shown on the campaign map just takes in acount the upkeep of your units, which is divided between your cities according to their population (a large city pays a larger share of the upkeep than a small city), so it may seem as if your more populated cities lost money, although they actually don't.

Could you perhaps post a screenshot of your campaign, so we may get a better idea of what's going on? My best guess at this time would be you have too expensive troops or ships to support.