That isn't at all how the skill works. The initial hit is 50% of your AP... And then every combo point spent within the next 12 seconds is another 10%. Lined up optimally, you get 3-4 finishers off in that time for another 150-200% (200-250% total).
I'd suggest actually learning your skills before trying to say they're bad. Or even watching the videos that I said to watch, that shows how to optimally burst with it.
eta: You're also completely disregarding the fact it has no energy cost, whereas the other 2 do. Not to mention the enormous haste buff... Further increasing flagellation's value. Good job.
eta2: You're also completely disregarding the fact that Flagellation's conduit buffs its damage a lot more than the other covenant conduits buff their respective abilities. Good job, again.