Congestion Relief Zone - charging even going over the Brooklyn bridge.

Can someone explain this to me? Why am I getting charged a Congestion Relief Zone toll ($9) when I am taking the “free way”. I live in the UWS and take my son to school in Brooklyn. I enter the FDR at 103rd street, I don’t exit the FDR and take it down to the Brooklyn Bridge. Where would I be getting charged at? I was under the impression this was a free route to Brooklyn.