[ghaff]

It's confusing the way it is written and there's no actual map but:

"In turn, that means drivers can enter Midtown and Lower Manhattan by two bridges without paying as long as they go directly to the F.D.R. Drive along the East River and then continue on it until they are out of the congestion zone."

I believe what they're saying is that you still enter the congestion zone via those two bridges but you can stay on FDR drive and exit the zone without getting on interior streets [ADDED: and not get charged. FDR Drive is the road that runs along the East River.]