New York State already has a major toll road (NY Thruway) and tolls to enter New York City. So do New Jersey and Connecticut, the other states you must drive through to enter New York City. The congestion pricing is a new charge on top of longstanding toll roads and bridge/tunnel tolls, so it feels like a new category and the start of something new, rather than being equated to "usage fees" as you state, at least in the minds of many drivers.
The people's intense response - from supporters to opponents - plus the media coverage and political posturing, demonstrates that it's not "simply another toll"