Are you happy? -- an objective question to which the speaker does not know the answer. Aren't you happy?-- a question asked by a speaker who thinks the listener is not happy.
They're both questions but there is an important difference. "Aren't you happy?" is like saying "I THOUGHT you WERE happy. Am I wrong?" The simple "Are you happy?" doesn't imply anything about what I thought, or expected; it's just a straight question.