Tsyr
Explorer
You answered that question yourself. It's magical. If there was a magical version of intimidate, PCs would be effected by that too, mostly likely. Magic trancends mundane things like "courage". Magical fear is pure fear pumped into the brain.
Personaly, I see it as much a courtesy to the player as anything, not having intimidate effect them. No, by the rules , you could have it effect them. But, as a player, if I was playing a really brave conan-esq fighter, or a "Bring it on!" dwarf or something, and the DM rolled to intimidate me with a charismatic-but-dinky halfing rogue, and said "Ok, your scared out of your wits by this guy, you pee your pants and start shaking", I would probably have some choice words for that DM.
Personaly, I see it as much a courtesy to the player as anything, not having intimidate effect them. No, by the rules , you could have it effect them. But, as a player, if I was playing a really brave conan-esq fighter, or a "Bring it on!" dwarf or something, and the DM rolled to intimidate me with a charismatic-but-dinky halfing rogue, and said "Ok, your scared out of your wits by this guy, you pee your pants and start shaking", I would probably have some choice words for that DM.