An anonymous reader points out a New York Times article about a traffic analysis program that
"'works by taking note of which cellphone tower a phone is communicating with. It then looks for disruptions in service followed by significant changes in location. If a phone located near Times Square suddenly loses service and reconnects at Prince Street and Broadway 15 minutes later, then it has almost certainly traveled there using the N or R trains.' In another interesting twist, the article briefly notes, 'The system will also include an experiment that uses phones' microphones to sense when riders are on buses.'"
The article also mentions a similar project to track buses and trains in Los Angeles.