Thanks to anyone who answers I was just wondering about this and thought you guys would know.
A possible explanation is that it's a reference to Christian Iconography in which Jesus sits to the right of God. The early Christians may have taken this imagery in turn from the Roman depictions of authority in which a speaker holds a scroll with his left hand and gestures with his right.
However, the phrase does not appear in English until the 17th c. so I can't be confident about the connection.
I couldn't find any better explanations though.
http://www.orthodoxartsjournal.org/authority-on-the-right-power-on-the-left/
The earliest I can find the term attested is in Greek religious practice, in which the right side was well-omened. In Roman augury it was the left hand that was a good omen, because Greek augurs and Roman augurs faced in opposite directions while watching signs, so a sign on the same side would be on opposite hands. In Latin (and I believe Greek, but I'll have to check on that) one can say that someone is on your right to mean that he's on your side, that he's protecting you. I've heard it suggested that this is a reference to military practice, since the guy on your right in any formation is the one who protects your unshielded side, but I find this explanation a bit lacking, since the phrase is almost always used religiously. Propertius, for example, describes both Bacchus and Apollo as being on his right side when he means that they are helping him and watching over him, and the phrase re-occurs rather frequently--as I recall, Virgil is rather fond of it. The well-omened aspect of the right side in Greek religion is very well-attested, and was so influential that even though Roman religious practice didn't change in colloquial speech it was customary to refer to the right as being the favorable side and the word for left, "sinister," eventually came to lose its original secondary meaning (favorable, or lucky) and take on its modern meaning
followup question: why was the right hand man so much more important than the left hand man in the military? (see rest of post for explination)
oed definition
†(a) a soldier holding a position of responsibility or command on the right of a troop of horse (obs.); (b) a person who serves as chief assistant or indispensable helper to another.
here is a 2007 local SD newspaper article which claims the term's origins are forgotten but in the 17th century cavalry officers who controlled the right flank of their force were so named.
and here is the use of the phrase in an old light cavalry manual where the term left-hand-man is also used. https://books.google.com/books?id=2UEIAAAAQAAJ&pg=PA21&lpg=PA21&dq=cavalry+unit+right+flank+discipline+right+hand+man&source=bl&ots=Ojb7gOzFX3&sig=qvZPia0o92tTbr3qw9kmvLFiG_g&hl=en&sa=X&ei=SibgVK67H9DxoAT2k4K4Ag&ved=0CCcQ6AEwAQ#v=onepage&q=cavalry%20unit%20right%20flank%20discipline%20right%20hand%20man&f=false
so given all of this i think it originated in 17th century cavalry organization due to the important role the right wing leader played say in maintaining discipline (still not sure exactly why)