It's simply accepted as a necessary path to understanding. Following this road, we've not only reduced Nature into smaller and smaller parts, we've reduced science itself to narrower and narrower academic specialties. The worldview of these disjointed disciplines is limited to highly constricted horizons that prevent even seeing into other disciplines, much less the whole of Nature. In short, normal science is a box of closed boxes. The problem is, to solve the puzzles of Nature, we need to see them from outside the box.
Reductive specialization invites perilous consequences.
Just as it precedes extinction in the natural selection of species, it foreshadows irrelevance in science. The irrelevance of normal science to living systems can be appreciated by reducing reductionism itself to absurdity. This is absurd because neutrons, protons, and electrons, the rudimentary parts of, say, possums, are also the rudimentary parts of every other material system. They don't entail possumness. The only justification for reductionism is the tacit assumption that it is reversible.