I agree with TFA’s premise, but some of the specific arguments present are faulty.
Flat vehicle registration fees
Excise tax is not flat, and sometimes a luxury tax on top even makes it progressive. These are registration fees paid to the town instead of the state.
The storm sewer subsidy
The complaint here is that pollution is contributed by commuters / travelers but cleanup is paid by locals. The travelers polluting city storm water sewers are paying taxes in the city when they do business in the city, which is why they are using the roads. If there was no reason to come to the city, there would be a lot less stormwater pollution but also a lot less commerce and the city would be worse off.
Insurance rates
The fact that everyone pays for their own insurance means that is it not a tax. If we subsidized insurance based on income, then insurance would effectively be an income tax. Which, by the way, is true for health insurance.
Gasoline and gas taxes
Are meant to cover (part of) the externalities of driving. The same as the congestion tax the article is supporting. By covering the externality we discourage the polluting activity, which is equitable to be done for everyone who is polluting, regardless of income.
EV tax credits
If we want these (cheaper, more economical, cleaner, safer) cars to become available in the mass market, there is a multi-billion dollar R&D hill to climb. Economies of scale for li-ion and electric drivetrains do not materialize overnight. Getting rich people to spend $60-$100k on a new toy to fund this endeavor, by providing a $7500 carrot, benefits the poor and middle class in the long run. Hell, it benefits the whole planet in the long run. The rich people are putting up a lot more capital than the Federal government in this equation to make mass scale EV a reality. This is a huge win and to say it is inequitable totally misses the point of the subsidy.