A big part of that is the devalued Yen, which is a recent phenomenon (~2-3y). Travelers with USD or EUR are going to think everything's cheap because of this.

But even ignoring the exchange rate (this is easy to do: just assume 100 yen = USD$1, like in the mid-2010s), most of the trains (or subways) are really cheap compared to costs I've seen in other countries (US/EU), and far better run on top of that.