No major US public transportation system is fully paid for by riders.

Yep. https://www.transitwiki.org/TransitWiki/index.php/Farebox_Re... is a sobering reminder that many cities’ public transportation would cost $20-50 per trip if paid entirely by riders and thus could not exist without subsidy.

That includes cars on public roads.

Neither is any private transportation system?

Public transportation is the backbone of a functioning economy. It doesn't need to be fully paid by riders precisely because the rest of society benefits from it multiple times over.

NYC congestion pricing seems to be working quite well though, and probably helps offset MTA costs.

NYC "congestion" pricing (actually cordon pricing) is a good idea. Would be great to see more road use fees proportional to use (distance, weight^3, etc.).