It's well understood by the locals that the Hong Kong (and possibly other Asian cities) system reaps most of it's revenue from land rights around/immediately above the stations. In

In Asia transit hubs are often also retail hubs and the commercial rents become profit for the public transit system. This makes perfect sense as the retail value of the nearby land can most obviously be credited to the transit system.

I'd imagine that the problem with the United States is that this real estate was sold early on or was never owned by by the transit system allowing the spillover benefits of transit hubs to be captured by private interests.

Yeah, majority of Hong Kong subway stations has malls on premise. Not sure it's owned by MTR too, but it's there.

Farebox recovery ratio is not a measure of net profit, it is a measure of operating profit specifically for transit assets, with only fares counting as revenues. In other words, the MTR's subway lines are profitable entirely by themselves. The real estate profits are just a cherry on top.

Isn't that part of the problem? Correct me if I'm wrong, but I recall hearing from someone that the MTA sold a good portion of its real estate and so lost sources of income.

I'm not all knowledgeable in this, so if someone who knows more of its history can chime in please do.