We don't expect roads to be profitable. We don't expect airports to be profitable. But there is a solution to this as well. If the train operator owns the land around each station and collects rent on the shops and homes, they can become profitable.
I sudoect that airports can be far more portable than airlines, actually, since shopping, eating and drinking are much cheaper to deliver on the ground. And there’s parking too.
One might have instead believed that because SFO is so valuable to the region it should be heavily subsidized, but the property repeated worldwide is that valuable things are things people don't mind paying to use. Because they're valuable.