The body mounted bars probably offer just as much protection from flying objects (rocks / sticks etc which are thrown around), but the body mounted bars can't support too much weight...... If you were to try and use them to slide your vehicle over an obstacle you would do significant damage.
Frame mounted bars can act as a skid plate of sorts..... they can be used to help slide the vehicle over large obstacles, they can also be used as a jacking point if you needed to lift the vehicle up to change a tire or something.
I haven't seen frame mounted bars on larger trucks, but I think they're still pretty common on mid sized trucks and SUVs..... It's been a while since I looked though.