The plan was structured in a way that it would affect every resident of the city via higher prices on goods and services, surcharges on delivery, taxis, construction, etc. Setting aside the issue of local residents with cars (which I could care less about), the planners refused to make sensible carve-outs for things like cargo trucks, construction vehicles, and so on. They could have done it, they just didn't. It was about maximizing revenue for the MTA, not about making sensible policy.
Maybe the fees would be small when amortized over a truck full of groceries or a tanker full of oil, but that didn't change the fact that it was a regressive tax on everyone who lives here, and taxes here are already amongst the highest in the country. This stuff adds up.