Passenger capacity is part of the design of air travel. Even so, a plane could be at 1/3rd capacity before it's less efficient than a singly-occupied car.
Trains are largely a relic of the Industrial Revolution - except for those places where population distribution has made it feasible to invest in specialised passenger rail, the degree of infrastructure investment required makes them economically infeasible given a blank slate today.
If we were really concerned about transport efficiency, long-distance bus routes are the answer. Per-seat energy usage is comparable to trains, but with a fraction of the infrastructure cost, and significantly more flexibility. Countries that have a blank slate and are only interested in maximum transport for minimum cost (ie, the developing world) have gone that way for a reason.
We accept nearly empty trains, despite them needing at least 30 passengers to be competitive from a fuel efficiency standpoint with a singly-occupied car, because trains are largely seen as a service. Very few passenger trains are economically viable without government support.