Agreed this fee is absurd. A couple years ago it was more like $4-6, though I believe the "concession charges" other airports charge is bundled into the $12 bus charge, so at least you aren't being double taxed.
Last time I rented at SFO I used Budget. The contract didn't include the $12 charge, and I asked the agent why that was. She didn't know, and I never got charged!