Don't put the cart before the horse. The Wikipedia article says that "The Metropolitan Transportation Authority (MTA) estimates $15 billion in available capital will be generated by bonding revenues from the tolls, which will be available to fund repairs and improvements to the subway, bus, and commuter rail systems."
My brother lived way out in Brooklyn and commuted to Manhattan for decades. Never had a car the entire time. Apparently New York's public transportation isn't a big issue.