Oddly enough, I think this was lightly touched on in the first Assassins Creed.
The theory is that the microchipping is something conceived by the Illuminati, who supposedly seek world domination by manipulating the worlds events from "behind the curtain". Their ultimate goal is to bring about a New World Order (rumored to be brought to fruition in 2012 hence the 'apocalypse' hyperbole), which would essentially strip people of their rights and beleifs, forcing them to conform to one universal way of thinking and acting. Including Christians. The link to the microchipping process and the religious fanatics has something to do with a relevant date or coincidental number involving 666 (the mark of the beast). This could be a factory production serial number or a date or something I'm not too clear on it, but I do know there is some kind of superstitious link.
Personally I think microchipping is a terrible idea that will severely worsten everyones views on the government and will probably kill off everyones right to privacy.
Microchipping notorious peadophiles and murderers is a good idea though.
It has its uses but they must be used properly, minimally, and on the right people.