FasTrak transponders are going to be used to collect data on driving times: basically, they'll silently ping your transponder for its ID, and see how long it took you to get from point A to point B. They claim that they hash the ID first, and that this hash is not reversible; however, it's still a uniquely-identifying cookie, since they need to know when they've seen you again.
They claim that if you wear a tinfoil
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511 Driving Times will give current driving times on Bay Area freeways between any two cities or major landmarks, through the 511 telephone number or the 511.org web site. This information will let drivers know how long it will take to drive through a backup, when they will reach their destination, or whether they will be late to work or home on a heavy traffic day. [...]
MTC has installed small antennas over freeways to read FasTrak toll tags (the small, credit card-sized device typically installed on car windshields). When a car with a FasTrak toll tag drives by an antenna, the system detects the presence of the toll tag. Unlike the antennas at the toll plazas, the antennas installed for 511 will not cause the toll tags to beep, so there will be no annoying noises for drivers. The 511 system immediately scrambles the toll tag's identification number in order to protect personal privacy. When that car passes the next 511 antenna, the system again detects the toll tag, and again scrambles it, using the same process. By averaging the travel times of all vehicles over a certain period, the system can calculate the average travel time and speed. [...]
MTC and Caltrans both guarantee that FasTrak users will remain anonymous. Encryption software scrambles each FasTrak toll tag ID number before any other processing happens; the set of scrambled IDs are discarded every day; and the encryption code is changed every day. No historical database of the encrypted IDs is maintained. No one involved in 511 will ever have access to the FasTrak ID number or any personal information related to the toll tag. None of the information collected for 511 Driving Times can ever be associated with a specific FasTrak account. Because of these protections, there is no way that 511 could be used to issue traffic tickets or otherwise "track" users. [...]
If you are uncomfortable with participating in the 511 Driving Times service, FasTrak will provide you with a Mylar bag. [...] When you insert your FasTrak toll tag into this bag, it cannot be read by the 511 antennas. However, you will need to take your FasTrak toll tag out of its bag to be read at toll plazas.