Flurry should get a damage boost but it makes 0 sense to add together the 3 attacks and list them as 1, because they behave as 3 separate attacks. You can miss on attack 1, 2, 3, or any combination of them, it isn't guaranteed that all 3 hit. You can crit on 1 and not 1 of the others. This is why it makes perfect sense to list only the damage of 1 hit. Furthermore, even if you are not good at basic multiplication, you can still make a tactical decision about whether or not to use it, without knowing exactly how much damage it will do. It goes something like this:
1) Do I have a better use for 3 AP? If yes, don't use Flurry.
2) Do I have a better use for 1 AP? If yes, don't use Flurry.
3) Will I have a better use next turn for either 3 or 1 AP? If yes, then don't use flurry.
4) Is my only option on either this turn or the next to do a basic attack or Flurry? If yes, definitely use Flurry.
Almost any 1 AP ability can be justified being used over flurry, you definitely won't be using flurry in the late game and it is likely something you will only be using in A1, if at all. I would rather remove my offhand and use sucker punch however, then use flurry.