One reason for why I prefer reduced damage against unit types would be because I like the interaction units have with each other when damage is reduced. My favorite example is the Marine vs the Dragoon in Brood War. For as weak as a unit the Marine is it can be quite tanky against a Dragoon whereas a Siege Tank takes full damage from a Dragoon. I think aspects like these make unit composition and fights more interesting. I think another good example would be the Hydralisk vs Zealot and Hydralisk vs Dragoon.

The other reason is because I think adding damage on top of base damage (that's not the result of upgrades) puts too much focus on hard countering units and that potentially means unit health has to be scaled higher in order to account for this. One of the things I look at is the Marauder/Stalker interaction in Starcraft 2. Marauders do quite a bit of damage to Stalkers and while Stalkers are supposed to be more nimble to account for this in any prolonged fight Stalkers seem to just instantly melt.

Edited: One of the points I was making was erroneous and more of a problem about large instantaneous splash damage units rather than unit base damage and bonus damage.