1) It's a regressive tax on everyone living here -- even if you never use a car. Literally everything we buy and use in the city gets more expensive because of this law.
2) That same regressive tax is used to provide a lifeline for an exceptionally wasteful public organization (the MTA) that needs budget discipline, not additional funding. The MTA rivals Tammany Hall in terms of waste and fraud, and the talks of budget cuts were political crocodile tears.
3) (more minor) By definition, the point of this tax is to make it so that only rich people can drive. As the article notes, of course this is great if you're rich enough to afford it...but the article doesn't quote the people who can't now.
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Edit: I'm just going to respond to the single point that everyone is making in one place, instead of repeating it: you don't just get to assert that the hypothesized "reduction in transit time" offsets the costs. You have to prove that argument.
You're the one arguing in favor of a new tax. It's not my job to prove the negative.
Ultimately, congestion was itself a cost, but it was a dynamic cost, increasing and decreasing with the amount of congestion to maximize utility of the roads. What the state has done here, effectively, is set the price of driving higher than the market at all times in order to guarantee a marginal reduction in demand.