The shadow clone jutsu shares chakra equally between the clones and the original, thus Naruto only has a small fraction of chakra left, which might not be enough to fly.
maybe it was a clone after all... that naruto sent in there, but the moment the clone went inside there it lost "connection" to naruto and lost the ability to float since only the main body can decide what floats or not?
Yeah it was a clone people may say that it isn't because he didn't disappear instantly but he wields the power of the Sage all his Jutsu are beyond Kage level now using So6p Senjutsu with Kagebunshin and Two tailed beasts thats a whole new level anyways know this he is not dead.
EDIT: Oh and also they probably thought Obito and Co were clones cause they disappeared BZ thinking they ran out of chakra because of the dimension chakra toll gate but infact Naruto's clone survived and it was Obito and Kakashi/Sakura.