Boeing is a publicly traded company based in the USA. That is different from being owned by the USA. Amtrak (which provided passenger rail service in the USA) is owned by the US Federal Government. Boeing on the other hand is owned by a multitude of individuals like you and me and probably a good number hedgefunds.

You could have the fines be "heavily" pulled out of compensation packages for the higher ups who actually have the power to change the organization... but then they'd probably just leave and screw up some other place?

Do boards generally try to claw back compensation in these sorts of situations? (Just as they have been doing in some of the recent cases involving financial shenanigans.)