I'll put this simple; You buy a Hotel. You're not supposed to pay the Hotel costs each week. You manage the Hotel, and it makes profit to you, enough for the expenses, and more into your bank account. If the Hotel doesn't make profit, why would you keep it? Better sell it away and save money.
I see FC as Hotels. They're supposed to be an investment. You're supposed to manage them, not work for them. You're supposed to HIRE people to work in them, and they are supposed to make profit.
So yes, FC's upkeep is rubish as long as they don't make meaningful profit with NPCs. Yes, the FC can take 25% of what players gain with cartographic data, bounties and bonds, etc..., plus the share, but I'm sure that depending on players to make profit is a weak expectation.
Using FCs to make profit with NPCs would even change the galaxy market for the better, because less people would stick to bulk trade, and markets wouldn't be so empty of high profit commodities. This kind of trade would be more used by med tier players, and FC owners wouldn't be so eager to bomb a station's market when selling excessive amounts of commodities.
I would use upkeep for one thing though, to allow a FC to be public - as in, visible and accessible to other players in Solo, Open or PGroups.
That way, there would be less FCs around in each system.