There are very very few places in nyc not accessible via some combo of bus, metro and ferry. It's not as reliable as say Japan but the public transit network is pretty extensive.
Not everyone who drives through NYC lives in NYC. Even if it were, those transit hops add time. Now you're forcing people to choose between paying money they don't have or spending time they don't have.
If you're driving through NYC you probably have enough money for gas and $9 and all the other tolls on the road. No one is driving around on their last drop of gas going "gosh I could just get out of Nyc to Long Island if I just had that $9 for gas".
The poor car owner who can't afford $9 stories are all made up nonsense. "Not everyone has $9 to spend to drive their tens of thousands of dollars car."
