Oh.... not to fret. A settlement always makes money. It's just that the 'income' you see already has troop upkeep deducted from it. Your army upkeep is split proportionately between your cities-- the higher the population, the more it pays. Conversely, the smaller it is, the less it pays. That's why you always see big cities with 'negative' income while small settlements can rake in positive income. A larger settlement almost always makes more money, it's just that they also shoulder a larger part of army upkeep.