"You have to go home" has the same meaning. "You are to go home" does not sound natural.
You have to go home - Musíš jít domů. There is a difference in it. Muset = must is a situation in which you are forced by circumstances or somebody's demand to do something. Mít + verb = supposed to , be to +verb is a request and it is up to you to decide if you are to follow it or not.
"You are to go home" sounds natural to me, at least in American English. For example, "you are to go home at 7 pm." The "supposed" is implied in such a sentence.