Runes got implemented very very poorly. Such a good idea and such bad implementation.
I am not sure if they get boosted by fortify dest, but the 1 rune at a time makes that strategy suffer.
If you are on the PC, I would suggest getting the "4 runes at a time" mod, along with a "balanced destruction mod" (I did)
That way you can place multiple runes, and they scale in damage as your skill increases.
right now 1 at a time for 50 is just silly beyond level 25 or so.
with those 2 mods, and runemaster, you may find yourself using runes almost exclusively.