While we should never expect public transit to be self funding removing fares removes the ability for transit funds to scale with ridership, there is a reason that farebox ratios are correlated with ridership.
In any case, cities can engage in value capture for public transportation. Just direct some of the property taxes collected directed to public transit. Even better would be some sort of LVT, ideally but not necessary 100% of the economic rent from land.
In any case, public transit should also engage in value capture on their own property. If they own a train station, they should consider building on top or adjacent to it spaces that they can then rent out to tenants. It's not only efficient but also serve the public and the local economy and making public transit more economical to run due to higher ridership.
Like airports in America. We should pursue a similar path for our rail stations and, frankly, ensure they are heading toward locations that are walkable and connected.
Almost every smaller station shows ads on walls, too, and every train carriers ads inside.
I don't see why the subway specifically could not be self-sufficient, or even a profit center. Sadly, this is not so, because of very large expenses, not because of low revenue.
And urban malls and chain stores are frankly often depressing — awkward layouts translated imperfectly from suburban sprawl, along with obviously underpaid and burned out staff.
Many companies in Tokyo prevent their employees from commuting by car (legally commute is covered by workers comp insurance, and many companies do not elect the more expensive car coverage option) - so even in the absence of workers paying for the commute, public transit (or bike/walk) would be the only realistic option.