As with so many of English's warts we can blame the French for the situation we're in. Vous in French is used when addressing a single person formally and conveys respect for the addressee. When class and station were more important following the Norman conquest of England, English speakers adopted the use of "you" to address a single person of higher status following the French custom. It's use became more widespread over time lest the speaker offend someone by using "thou" when the addressee thought that "you" was warranted.
As a practical matter, I use y'all. I think thou is a lovely word in its own right and is deserving of consideration.
N.b. IANALinguist, and IANAHistorian either. TINLinguisticA.