It is certainly correct that having fixed fares across time and distance is a government subsidy which arguably may even effectively target poor riders.
The lack of a subsidy is fundamentally not the same as a tax.
But when a subsidy distorts the market to the point where it causes inefficiencies in the market, those inefficiencies can undermine the value or effectiveness of the subsidy, sometimes altogether.
I.e. lack of peek pricing causing massive ridership spikes at specific hours overloading the system and making it break down.
A theoretically better system might be one with a fixed monthly fare credit for low income riders, while also having peek pricing. This shifts demand to keep the system running more smoothly while also making transit more affordable for lower income riders.
But then, why not ask the question, if we’re giving money to low income riders, why give rebates only to low income people who ride the train? Why have a low income subsidy specifically for subway ridership versus any of a dozen other things people fundamentally need. Why micromanage to that level?
Fares in Osaka or Tokyo are ~$2 per 3-4 stations from your departure point. Riding to Kyoto from downtown Osaka (40km) is ~$8 and 8 stops across two lines. The prices overall are low (IMO), and Japan has lower wage inequality than the US (IIRC).