[B.T.]

In many situations, a prone character is harder to hit, if he is, as an example, behind some low cover. If you roll for hit-location, a body part behind cover, cannot be wounded or is protected in those "hidden" areas.
Example: The character goes prone behind a low wall. Depending on GM judgement (heights of the wall, etc.), the legs, the abdomen and maybe even the chest or the arm(s) would be behind cover. If the attacking character rolls for hit location and comes up with a hit on those locations behind cover, the bullet may be too weak, to pierce the cover: The chances for a person, to be hit, is lower. (You have to compare the armor value of the cover with the damage of the weapon/ammunition.)
Another situation, where going prone may be a good idea is, when a character want's to fire a weapon with an attached bipod. If the firer is standing, he cannot rest the bipod on anything, if he goes prone, he may find a rest for the bipod.
And you can hurl grenades over a cover and avoid being "hit" by the concussion and the fragments.
Still another thing to mention: Going prone can be an effective way to hide. If a person is going prone behind a bunch of bushes, small walls, or the like, the attacker(s) or observer(s) may not see their target anymore.