"drivers would not have to pay if they entered Manhattan
by all but two of the city-owned East River bridges,
which are now free to cross, as long as they bypassed
the congestion zone."
I don't think I understand this part. Why would you have to pay if you "bypass the congestion zone"? no matter where you're coming from. Now, if what this means is that you don't have to pay the $11.52 fee after having already paid the $15 (if you pay cash) for the toll fee coming from New Jersey, makes sense.