The Barberi and Austen classes do not carry cars, however since the Kennedy class is still around that wasn't really much of a problem.
The ferry only stopped carrying cars because of Sept. 11th. Originally I thought it was because it would be pointless, what with no driving allowed downtown anyway. Clearly there are other reasons since it's 2 years later, but since I don't know for sure what the reasons are, just heresay, I'm not going to bother.
The new class was ordered and designed *BEFORE* September 11th, to replace the Kennedy class. Since the only money made on the ferries is in food service and transporting motor vehicles and bikes, and people would complain at the loss of the cheapest way to get your car to manhattan, it'd be insane to replace car-carrying boats with more passenger-only ones. After all, they have enough of those floating around...