Nowadays the term pagan had become almost synonymous with devil worship - a gross misconception. The word's roots actually reached back to the Latin paganus, meaning country-dwellers. "Pagans" were literally the unindoctrinated country-folk who clung to the old, rural religions of Nature worship. In fact, so strong was the Church's fear of those who lived in the rural villes that the once innocuous word for "villager" - villain - came to mean a wicked soul.
t is true that the word 'pagan' comes from the Latin paganus, meaning a rustic or country-dweller. The etymology Brown gives here is also commonly held, but not exclusive.

It may be that non-Christians became known as pagani because the country-dwellers stuck to the older religious traditions longer than city folk. New religions often spread via trade routes and are taken up more quickly in urban centres along those routes than in more remote areas. The alternative etymology, however, is that the term came from Roman military slang, with the word originally meaning 'country bumpkin, civilian or incompetent soldier'. According to this theory, it became part of the terminology of early Christianity in much the same way other military imagery did, with believers calling themselves milites, or soldiers of Christ.

Brown's choice of wording here is also interesting - the pagani of the countryside were 'unindoctrinated', implying that the Christians of the towns were therefore 'indoctrinated'. The implication here is that, somehow, Christianity was foisted on people like a form of mind-control. The 'unindoctrinated' pagani on the other hand, practiced 'Nature worship', which sounds much more pleasant and bucolic than a religion which requires 'indoctrination'.

This implication is further underlined by his talk of 'the Church's fear' of the unconverted pagans. He says that 'villain' became a word meaning a criminal or miscreant because of the Church's fear of paganism. In fact, the word simply means 'farmhand', from the Old French villain and the Latin villanus, related to the Latin villa, 'country house'. It is a pure piece of snobbery aimed at country people and one that arose in a period in medieval English history where there was migration of country folk to the towns. It has no more connection to 'paganism' than any other such word with similar origins and meaning - eg 'churl' - and first appears almost one thousand years after country people were likely to be pagans in any sense of the word
http://www.historyvsthedavincicode.com/chaptersix.htm