The argument being used is pointing out that roads are only sustainable financially because everyone is subsidizing them. The same applies for many subway systems and other forms of public transit.

Transit is only not sustainable because too few people are using them.

Then why are the only two in the world that bring in more money than they take in Japan? Surely people in other countries heavily depend on them.

Firstly, there are more transit operators that are considered profitable outside of Japan (for example Hong Kong, Singapore).

Secondly, it depends a lot on accounting. Consider that in Europe, most infrastructure doesn't get built until it has a positive cost-benefit ratio. Since transit does get build, it's overall positive economic impact apparently outweighs the cost - so overall they do 'bring in' more money than they take.

Thirdly, if you require a strict sense of 'bringing in more money than they take' as a specific organization building the infrastructure then charging for the access, I have to tell you that there are relatively few roads that 'make money'. In fact it's basically only some highways, and bridges -- high capacity trunk lines, and lines across choke points. This ignores the cost of large feeder networks, which are generally paid for by taxes. In North America, municipal taxes. This gets interesting when people who don't have cars subsidize single occupancy drivers via municipal taxes.

If you ignore feeder networks for transit, for example ignoring the cost of bus feeders, and only considering the cost of major trunk lines relative to the income of the whole system, then I'd say many subway systems in the world 'bring in more money than they take'.