Eric--- The reasoning I've heard in our marina for the factoring in of a boat's footprint into the slip fee formula is that in recent years a lot of sailboat makes and models have gotten really wide. In some cases, so wide that it makes it difficult to impossible to put a second boat in the slip with it. So the port loses the income from that empty space next to the opposite finger pier.
Also, for awhile it looked like catamarans (power and sail) were becoming pretty popular. That initial surge in popularlity seems to have dwindled and died, at least in our marina. But I'm sure the port was getting concerned at one point about catamarans making it impossible for two boats to share the slip.
I'm not saying the port's decision was justified, but it's what they did.
And in Bellngham, it's my understanding that the marina has to be entirely self-sufficient. In other words, tax revenue cannot be used to support the marina. And we all know that costs of everything from electricity to garbage collection only go one way: up. But since tax revenues cannot be diverted to the marina, every increasing cost of running, maintaining, and improviing the marina has to be paid by revenues collected by the marina.
Some of this revenue comes from businesses leasing buildings or space on marina property--- restaurants, charter companies, the big Seaview North boatyard, and so on. But it also comes from the folks who keep their boats in the marina.
So it's a Catch-22. Marina tennants want good upkeep, repairs, and improvements. But that means they have to be willing to chip in and help pay for them. So we do, and then we complain about the rising cost of moorage, or the new slip fee formula that gets the marina more income.