The article says that they anonymize the IDs and the traffic management systems aren’t linked to the EZPass user databases. It actually sounds like they’ve made at least some attempt to take privacy concerns into account while collecting incredibly useful traffic management data.
That said, I imagine the right kind of government agency could probably still get access to the data and reverse the anonymization to link it up to the EZPass user data.
But at the end of the day, while there are some scary privacy implications of EZPass, if you’re driving a car you’re already announcing your location to the authorities with your legally mandated license plate. Almost every toll plaza is taking a picture of your license plate whether you use EZPass or not, and NYPD has license plate readers all over the place (including in many patrol cars equipped with real time license plate scanners). So I’m really not sure what privacy I’m giving up by using EZPass to pay my tolls. And having the ability to bypass the cash lanes (or use the car pool discount to knock almost $9 off each Hudson river crossing vs. the cash rate) is awfully attractive.