Scholars find the origin and root meaning of NTR to be a mystery to them.
Normand Ellis in her book The Union of Isis and Thoth
proposes one theory - that it means to identify the divine consciousness in everything and that it gave birth to the Latin word Natura, meaning Nature. She makes an interesting observation about flags. They have been commonly used outside of Egyptian and Hindu temples to show a god's presence. She connects this with the goddess Neith (spelled NT in hieroglyphics), as NT is part of the word meaning to weave:
The flag as a symbol of the presence of any divine being - god or goddess - harkens back to one of the oldest goddesses, Neith, the weaver. .... N-t in hieroglyphics also is part of the word meaning to knit or to weave, or to net. In Alexandria, the cosmopolis of ancient cultures where many languages merged, the ancient Egyptian word neter... the essence of the Latin word for nature, natura, emerged. The meaning was to identify the divine consciousness in all things. What do you think about her theory?
A weakness I see is that she is not a major Egyptologist, and her connection doesn't seem to be direct.
It's true that I think Neith probably is related to the word NTR, but this is not because flags are woven, but rather because her name sounds like NTR (minus the R) and because she was considered a major heavens goddess.
I don't know that the word for flag is NT or NTR in Egyptian and doubt it. Normand's thesis seems to be that flags show a divine presence and flags are woven, so the weaving goddess' name NT came to be used as a general word for God. But this seems rather an indirect connection. "God" or NTR does not directly mean simply "woven" or something woven. There are plenty of things woven besides flags.
What is your opinion on her theory?
Next I will give my own theory of the root for NTR.