The Anti-Planner argues that mass transit will never be energy efficient, mainly because it is virtually impossible to improve occupancy. The arguments for transit saving money all tend to include the line "will be efficient when occupancies increase" but he shows pretty clearly why that is probably not going to happen.
Also note pages 2-15 and 2-16 of this report. Compare the trends of auto and airline energy intensity with rail and bus. While cars and planes have decreased their energy use per passenger mile by quite a bit, rail has been flat and buses have been getting worse. In fact, auto transit became more energy efficient than buses twenty years ago and continues to get better. Airline travel has become nearly as energy efficient as Amtrak.