I'll give you five good ways to run them:
1. Combo charge with knights. Maximizing both units means that you can position flaggies for maximum carnage while forcing a couple files of the enemy to throw their attacks into 1+ AS knights.
2. Buff 'em. Light, Beasts, Life, War Altar... take your pick.
3. The flagellant wave. Take two small units ( I like 14 in 2 ranks), line them up one behind the other. The first unit goes in, does carnage and when it wimps out or gets wiped out in the next turn or two of combat, you've got a fresh wave of 14 flagellants. There are very few units in the game that can withstand 2 first rounds of combat with a unit of flagellants.
4. Screen them. An cheap detachment makes an excellent screen, breaking up LoS or granting them a much needed hard cover bonus. The detachment can then combo charge, or charge out of the way. Alternately the detachment can flee without panicking the flagellants behind them, either forcing a redirect or setting up a nice counter charge. Keep a stubborn unit with a lot of wounds nearby as the potential redirect target for your opponent and you can have a devastating counter charge.
5. Clear buildings. They fight with S5 every round they fight!
All that said, there's much less complicated and much more reliable ways to accomplish much of the above without using flagellants. Still, they're pretty tactically fun!