Being lord of a rich city *does* entitle you to make more gold than being the lord of a rural region. That's the way it's *supposed* to be. If the system results in the Margrave of a rich city and the Count of a rural making the same net amount in tax income, then the system is *broken*.
This isn't some hippy commune system we're trying to recreate, where everyone shares and shares alike. It's a system with inherent inequalities. These are fully intentional, and desired. You want to make more gold? Then move up the system to a better region.