While Shakespeare was using thou or you to make the formal/informal distinctions.
As this distinction signified respect, it would have been something of a social faux pas when the convention was broken. A master addressing a servant with you might have raised eyebrows in the thirteenth century. Among the upper class, using thou could have been considered a sign of disrespect. For a subordinate to use thou when addressing a superior, however, such familiarity would at best be considered presumptuous—and more likely boorish. Likewise, the use of thou could be considered condescending or insulting when used in a more formal situation.
The clearest example of this in Shakespeare is Sir Toby Belch's line in Twelfth Night, when he eggs on Sir Andrew Aguecheek to challenge Viola with "if thou thou'st him some thrice, it shall not be amiss." Not only is Sir Toby telling Sir Andrew to insult Viola with thou, Sir Toby himself is slyly insulting Sir Andrew by using thou with his peer. Shakespeare intentionally plays upon the significance of thou in this scene.
With the beginning of Early Modern English in the fifteenth century, however, the distinction was already becoming lost as you began to supplant thou as the only second person pronoun. By the time Shakespeare was writing, the inconsistency of his usage tells us that the process was already underway. For instance, Shakespeare often uses ye and you interchangeably, and there are instances of close friends or lovers calling each other you as well as thou—sometimes within the same speech.
Thou was essentially extinct in standard English usage by the 1700s. One of the main reasons thou survives at all is Tyndale's translations of the Bible into English in the early sixteenth century. In his translations (for which he was condemned to die at the stake in 1536), Tyndale returned to the simpler convention of Old English, consistently using thou in singular usage and ye in plural usage. As Tyndale's work became the foundation for the King James version of the Bible in 1611, thou was preserved for posterity.
http://www.bardweb.net/content/thou.htmlExample of 'thou' used to a 'superior': Joseph's brothers, trying to be humble to the Egyptian pharaoh - Genesis 47:3-4:
And Pharaoh said unto his brethren, What is your occupation? And they said unto Pharaoh, Thy servants are shepherds, both we, and also our fathers.
They said morever unto Pharaoh, For to sojourn in the land are we come; for thy servants have no pasture for their flocks; for the famine is sore in the land of Canaan: now therefore, we pray thee, let thy servants dwell in the land of Goshen.