Are you nuts? = Are you crazy?

The American language tends to do this where we will say things that wouldn't make sense to foreigners studying the language. "are you nuts" is simply asking if they person is crazy. They could be asking the sentence because they person may have done something they would think is stupid or if they didn't agree with what the person did.

isnt the english language confusing you think u got it down pat but then something new comes and slaps u in the face xD kkkk

A hard nut to crack.

In the 1800's "nut" meant a person's head, and around the same time it was decided that someone not quite right in the old noggin was "off his nut" or simply "nuts."