William Longchamp is credited with its introduction to England in the late 12th century, following the practice of the Chancery of Apostolic Briefs.[2] Its first recorded use was in 1169 when King Henry II, hard pressed by his barons over the Investiture Controversy, assumed the common theory of "divine right of kings", that the monarch acted conjointly with the deity. Hence, he used "we", meaning "God and I...". Wikpedia


The above explanation of it referring to god is very plausible, however I was taught a different meaning where "we" refers to the whole country. Since the king dictates what the government does, and by extension what the country does, his decisions are the same as the country's decision. I would not be surprised if it held different meanings for different rulers.