Question

Someone is knocking on/at the door.
Inside, we say, 'Who is it?' Can't we use, 'Who are you?' Is it rude to say, 'Who are you?
(Can we use both prepositions, on and at here? Are both have the same meaning? what about the next question?)

Answer 1

It is the same of meaning, but it is to rude to say who are you.

Answer 2

Mamoth is almost right.

You'd ask "Who are you?" if you really don't want to let the other person in because you don't recognize him/her.