The NY EZPass website allows you to register multiple cars for a single EZPass account (not sure about other states' EZPass websites). When I first got my EZPass, I would always add rental cars as soon as I picked them up. Then there were a couple times when the website said the rental car in question was already associated with someone else's EZPass account and wouldn't let me add them. I used my EZPass anyway, and haven't had a problem.

In theory I think they can fine you for improper use, but I have yet to run into any problem. They seem to have no problem billing my account for the tolls I go through no matter what car I'm in.