It depends on the circumstances. Until the late 19th century, with a few exceptions, armies usually fought in the open, standing up. The costliness of this tactic increased with the advent of repeating rifles and improved artillery, from the South African Wars onwards. At Spion Kop, for example, firing prone was the only way to have a chance of surviving. Once trench warfare caught on men didn't lie down in trenches, but in 1914 and, especially, 1918 lying prone became more common because of the type of warfare, using temporary cover to a much greater extent. Most European armies were issued with entrenching tools, for digging temporary 'scrapes', in the first decade of the 20th century. In North Africa in WWII lying prone became very common because of the lack of natural cover and the difficulty of digging trenches. Post-WWII it has, again, depended on the terrain.
But I would agree that up to about the FPW prone figures are pretty unrepresentative.