"You are being rude" can only be said while the person addressed is behaving badly.
"You are rude" can be said at any time after you have concluded that the person addressed is generally a rude person. This may be after a long while observing the behavior of that person, or it may be an immediate reaction.
Another way to look at it is "temporary and permanent" or "states and traits":
"You are being rude" tells how the person is behaving at the moment (current state; temporary)
"You are rude" tells how the person behaves characteristically (personal trait; permanent).