Yes I found this confusing, you have to look at your settlement details to figure out what is going on, but broadly as said above the main reason for a "loss" is that this settlement has a large population and hence gets allocated a large proportion of your armies upkeep.

As a corollary the campaign map income indicators are downright misleading IMHO , they should reflect that that place is doing well not that it pays a big swag out for armies upkeep across your empire.

Till it gets changed (not a bug) either formally or by modding the only really important figure is your overall profit for your empire.