It's part of Midtown in Motion, an initiative to feed information from lots of sensors into New York's traffic management center. A spokesperson for the New York Department of Transportation, Scott Gastel, says the E-Z Pass readers are on highways across the city, and on streets in Manhattan, Brooklyn and Staten Island, and have been in use for years. The city uses the data from the readers to provide real-time traffic information, as for this tool.
Maybe so, but, as the article cites, the EZ-Pass terms and conditions do not state that this is a permitted use of the device. And if one agency is using it for one purpose, you can be sure that in the future, more agencies in more jurisdictions will use it for more purposes, and some may be a lot more intrusive than dynamically adjusting on-line traffic maps.
I never got EZ-Pass, because I don't travel through toll booths that often, and I don't like the idea of paying a monthly service fee to have the device. With this piece of news, now I think I've got a much stronger reason than "I don't want to pay for it."