Most of the calories burned are just maintaining body temperature, pumping blood, and breathing. That’s around 1300 calories per day on average. The rest of the daily average is your daily movement.
The reason running a mile is only 100 calories or so is because it is only 15-20 minutes of moving your weight along the ground, and human evolution made us remarkably efficient at it. You only burn slightly more running than walking because roughly the same amount of work is being done in a physics sense. Plus the more you run the more efficient your body gets.
Your bodily functions run 24 hours per day. Running for 24 hours ~~which is impossible as far as i know,~~ would be 9600 additional calories. So it’s not really a matter of how little calories you burn running, but more that it is just a small amount of time comparatively.
Edit – see below
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