No Alkiviadis, it's not just the troops that are garrisoned there that are being paid. Each city pays a percentage of the upkeep of ALL your troops/agents/fleets equal to the percentage of your total population living in that city. In your case I suspect Rhodos and Thermon are quite large, so they're paying a large part of the upkeep.

An example: say you have one really large city (your capital) with 30,000 inhabitants and 6 small ones with 5,000 inhabitants each, making your total population 60,000 people. Because half of the population lives in your capital, that city will pay half the upkeep of all your troops/ships/agents, irregardless of where they are or what they are doing (like acting as a garrison of another city). So most likely your capital will 'lose' money fast, but the other cities (who are only paying 1/12th of the upkeep each) make up for this. That's why you really shouldn't pay any attention at the numbers you see for each city, but only look at the total. If over all you're making money it's all good, otherwise you'll have a problem soon :)