Just like playing tennis or golf on your wii isn't quite the real thing. Why is it that for arcade games (think Doom for instance), the disconnect with reality is not as noticeable?
You raise an interesting point. At a guess, I imagine if you asked a big game hunter or combat soldier with experience tracking a target and firing weapons with the intent to kill, they would probably notice the disconnect. I wonder if Guitar Hero has limited fans among those who can actually play the guitar, for this reason as well?
1) Your character gets tired.
2) You can't jump too high.
3) You can't carry 25 guns including a bazooka, sniper rifle and grenade launcher.
4) Reloading would take a long time.
5) If you jump off a ledge you get hurt.
Etc...
I think people notice its off, but ignore it in favor of having a good time. Eventually, if you play a game long enough, you might forget what you noticed, but thats more a result of playing a lot.