Just following up in case anyone else stumbles on this thread. I spoke to Rick Gardner from Caribbean Sky Tours, who was extremely helpful. I highly recommend that organization for great information about flying to the Caribbean and Mexico and Central America. I'll quote liberally from his e-mail:
"These fees are definitely outrageous and unacceptable. Here is the situation. San Jose del Cabo / “Los Cabo” (MMSD) and Puerto Vallarta (MMPR) are both government airports run by private companies under a concession granted by the Mexican Federal Government. In addition at MMPR there is an FBO which has the highest fees in all of Mexico (and the Caribbean as well for that matter). However, at both airports there is General Aviation Parking (Aviación General) which is available to pilots like yourself. You DO NOT have to use the Aerotron FBO.
In the case of Cabo San Lucas (MMSL) this is a privately owned and operated airport which does not receive any Federal subsidies and has the liberty of setting their own rates.
...
The MMSD quote should be about US$ 8 for landing, another US$ 9 for loading and unloading and then approximately US$ 10 per night for parking. Again all of this plus 16%."
I called MMSD at the number that Rick had provided me. At first I was told that the fees were $25-28 per day for parking with another $65 per person charge, which was way out of line with what Rick had said to expect. The person I was speaking with then said something like "let me check" and he came back with $10 landing fee, $6-7 per passenger and $11/day for parking, which sounds right in line with what Rick had quoted. It sounds like (and I sure hope) that the handling fee at the FBO is not necessary.
As for MMPR, I called and spoke with an employee at the airport (after a lot of runaround). According to her the landing and parking fees combined at MMPR are about 455 pesos for the week or 65 pesos per day, which seems quite reasonable (about $35 for the entire week). No per passenger fees, thank god.