Most of the bridges and tunnels have their own tolls, with a few exceptions like the Brooklyn and Manhattan bridges. One possible explanation is that the advocates were right and the combined bridge/tunnel + congestion toll is enough to dissuade driving into the zone entirely for people arriving via bridge/tunnel, but the lower congestion toll on its own isn't as much of a deterrent if you have access to a free crossing into Manhattan from other boros or were already in Manhattan (outsize of the zone) to begin with.