Edit: Now you've clarified your question.

There's nothing special about HSR when considering fuel (or energy) efficiency, except that it's probably less efficient over all due to increased air drag, and that it needs very particular infrastructure and passenger demand to make it work.

I'd hazard a guess that many (most?) flight routes are nowhere near popular enough to make them viable for train replacement.

Eg. The bullet train in Japan has a peak capacity of over 20,000 passengers per hour.

The most popular flight route in the US has around 3 million passengers per year, or ~340 an hour.