Some hybrid owners were also troubled by the notion that if they carpool on the bridges, FasTrak will ding them for what ought to be a free trip. MTC regulations give carpoolers -- three or more in a vehicle -- a free ride over its bridges.
Not to worry, said Goodwin. Your transponder, attached to the dash with Velcro, comes with a Mylar bag. "That prevents the signal from being read," he said. "Put it in the bag and you're good to go."
Sounds like you still need to have 3 bodies in the car to qualify for toll-free bridging.
EDIT: Yup, per URL provided by mcl in comments, you can drive across in the diamond lane, but must pay toll, hence the Fastrak requirement:
However, unlike HOVs or super-clean alternative fuel and electric-powered vehicles, which are allowed to drive toll-free across the toll bridges during designated carpool hours, single-occupancy hybrid vehicles must still pay tolls (using FasTrak™) when driving across the Bay Area toll bridges in an HOV/carpool lane.