How about the average person's commute time, or cost of living? Disclaimer: I did not read this article. I don't need to in order to state the obvious but there is a tiny chance someone thought about the impact on people overall.
I think the metrics are incomplete, if they suggest nothing but upside. Clearly, if people who used to drive wanted to take the subway and now take it, they could have done it before. So their quality of life must necessarily be lower, as they cannot use their preferred method of travel. And nevermind commutes. There are other activities that can be done with cars, such as moving your family around or shopping, that are objectively harder if you take the subway. Some people are probably paying more for groceries and other staples just because the cost of driving to a store is now higher.
I also bet that people who live in the city are paying more to leave the city for recreation or visiting family, or whatever. Once you leave the city you NEED a car, and you need a car to carry luggage too. So their quality of life is reduced in this way too. I doubt that the cost of upkeep for a car is higher than renting a car for a few days a month.
"The measure is failing because people are less able to do the thing that the measure was specifically implemented to reduce" doesn't seem to me like a very convincing argument.
The point is, there are obvious negative externalities to any intervention. It may be very effective at reducing congestion, at the cost of everyone's money and free time. If you can afford to pay all fees like nothing then it only improves your quality of life.