In the 6th ed Flagellants were ex soldiers driven mad by their experiences. They were believers in the end times - and were right, in a sense! 6th ed Flagellant sculpts have pieces of armour to show this.
3rd to 5th ed Flagellants had more of a Sigmarite undertone, and self flagellation was a big theme. The Marauder Flagellant sculpts were basically mad warrior monks, with books and blunt weapons. Close to the classic Blanche illustrations. The new plastic ones of the 7th and 8th editions seem to largely follow this idea. They focus on the madness, and this aspect was also emphasized in the later writing and rules.
http://www.solegends.com/marauder/mm65flagellants.htmEarlier still there were the Disciples of the Red Redemption, who were the initial idea that led to the later flagellants:
http://www.solegends.com/citrr/1rr16redemption/index.htmIf you want to emphasize the monk aspect, you can paint the robes with a single colour scheme. Black, grey, white, red, whatever. Maybe a nice contrasting colour, like some medieval monastic orders did.
Madmen can wear anything, simple or extravagant. Total freedom.
If you want to emphasize the ex soldier aspect, you can paint the robes or parts of the robes to echo various provincial uniforms.
Very free, but also a great opportunity for storytelling in figure painting.
-Z