Thou/thee/thy/thine are singular forms, whereas you/ye/your are plural. Just as we and our became royal pronouns, where a monarch would emphasize that they spoke for a whole country by referring to themselves in the plural, it became popular for the upper and eventually middle classes to refer to each other as plural, as a more respectful or formal usage.
Quoting from Wikipedia (http://en.wikipedia.org/wiki/Thou):
"Following a process found in other Indo-European languages, thou was later used to express intimacy, familiarity, or even disrespect, while another pronoun, you, the oblique/objective form of ye, was used for formal circumstances"