Yes, and so ? The article say NO OTHER non-profit is charged the fee. This implied the Sea Scouts are a nonprofit. And unlike other nonprofits, they're being charged a fee. So that answers your earlier question of whether they're being treated differently. They ARE being treated differently from other non-profits, because Berkeley doesn't like them. Your distinction between private and nonprofit is irrelevant. It just seems you're trying to invent an argument that could justify Berkeley's policy. Apparently you don't like the Sea Scouts either.
It's very relevant. As a private organization, it's nonprofit status is irrelvant -- private organizations should not be funded or subsidized with public funds. I don't care if it's the Sea Scouts, the KKK, Free Republic, or the Smith Family Reunion -- non-profit or not, if it isn't open to the public, then they have no right or reason to expect public support.