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.

Neither is any private transportation system?

That includes cars on public roads.

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.).