Keith Thomas, Religion and the Decline of Magic, observes that Reformation anti-Catholic propaganda sometimes depicts monks (holding candles, chanting, etc.) as devil-worshippers. The real root of the hooded chanting cultists in popular imagination, though, is in Gothic literature.

The re/naissance of the Gothic in the 18th century reflects the ambivalence of the Enlightenment: here we are, throwing off the bonds of idolatry and superstition...but at the same time, religion remained a fundamental aspect of life. The rise of the gothic likewise coincided with important political events: a long-running Spanish/English antagonism through the 18C, and tumult in France between various Catholic orders.

And so gothic-mode authors in Protestant England, Catholic France, and multiconfessional Germany all turned towards the Jesuit and the Dominican Inquisitor for their creepy bad guys. Monastic life in a pre-electricity age was based around chanting the liturgy in Latin (so, a "foreign language"), at nighttime lit by candles, wearing monastic habits. Mix in some anti-Catholic or anti-Jesuit feelings, the lurking supernatural evil that creeps throughout the gothic, and you have your archetypal cultists.

People went on to treat this image both factually and satirically. So the KKK adopts the robes and the ceremony; Animal House gives us the ritual initiation. The "Satanic panic" of the 1970s-80s envisioned its targets this way; Mel Brooks revived the Gothic version of the Spanish Inquisition.