There is a balance to be made. Certainly in Vietnam transport aircraft were lost due to small arms fire taking out the pilot and the Huey crews used body armour. Without wishing to turn the thing into an armoured bathtub there must be a need for some kind of personnal protection to pilots operating at low altitude.
As regards higher levels - in the case of the Vietnam war the U.S aircraft were operating against a sophisticated air defence network with the ability to fix damage sustained quite quickly.
Over Iraq however I guess the problem is MANPADS and AAA fire
which to some degree altitude cannot stop but can allow thinking time in which to react. The sad thing is that it's war zone and no matter what reports are done into it - it won't bring back the crew or indeed get rid of the chances of it happening again.