This (like most other flat consumption taxes) is a regressive tax. It is a stated policy goal of the ruling party to reduce income inequality, not increase it.

The disabled are a group with very inflexible transportation demand, in that they are very unlikely to change their behavior in response to higher prices (because they can't); we already make a whole ton of legal accommodations for them like handicapped parking, and this fits into that overall policy.

Unfortunately, this sort of thinking has been the dominant mode in politics and legislation since, I dunno, the Roman empire? Riddle your laws and regulations and tax-codes with exemptions and deductions and carve-outs so you can please the people who put you in power and who will keep your in power. And since almost everyone is part of some random interest group (and many, part of a lot interests groups like married home-owning couples with kids), it usually works.

There's also that not all vehicles are going to tear up roads in the same way. Why would it be fair for trucks and what not to pay the same flat fee despite causing far more wear and tear on the roads?

Your argument would result in the poor and disabled being priced out of driving on the road.

Congestion dynamics don't care about your income. Same imposition on society, same scarce good consumed, same price to get the incentives right.

Which sounds fairer to you: a movie theater that charges $5 for a ticket, or one that charges a percentage of your income?

People can choose whether or not to purchase a ticket. Many people cannot choose whether or not to drive. Which is why again, a flat tax would not be fair.

How would it be fair to expect someone on minimum wage or disability to pay the same amount to access a required service as someone far better off?