It was just another jutsu.
Only shinobi (Ninja) that were able to fly, float, disappear, etc.
Normal people cannot do that.
There were no Samurai that could float. (unless i had mistaken).
Tobirama & Minato could travel by S/T technique.
If that ninja had not enough chakra, then that ninja had to walk, run;
When Naruto used up the chakra (SM & BM), he was just in normal ninja.
i would assume that it's the number of element mixtures in the TSBs that allow for flight, since it was more or less suggested with Muu and Onoki's ability to fly being connected with their KT.