Basically, that part of the interface was designed by a retarted monkey.
Truer words were never spoken

You can see what your city actually is generating for income by looking at the trade sheet. There's an icon in the city view screen for it. What you see on the campaign map is what Ratwar is describing.....the distributed cost shouldered by that particular city, not what it is actually generating.

And as mentioned, as long as your treasury is showing a profit on the financial screen, you needn't worry about those seemingly negative income figures.