Why is Custom not Natural?

Carl L. Becker's The Heavenly City of the Eighteenth-Century Philosophers (1932) is a classic exploration of the modes of the medieval world that influenced the Enlightenment. At one point Becker contemplates John Locke's An Essay Concerning Human Understanding and observes that Locke's signal contribution was to show his contemporaries that since God had created nature it followed that the mind of men could be brought into "harmony with the universal natural order". Becker then observes:-

I need not say that the difficulties were great: endless difficulties in the realm of practice; one fundamental difficulty in the realm of theory. Hidden away in the elaborate structure of Locke's Essay was a most disconcerting corollary. It was this: if nature be the work of God, and man the product of nature, then all that man does and thinks, all that he has ever done or thought, must be natural, too, and in accord with the laws of nature and of nature's God. Pascal had long since asked the fundamental question "Why is custom not natural?" Why, indeed! But if all is natural, then how could man and his customs ever be out of harmony with nature? No doubt the difficulty could be avoided by  that there was not disharmony. (p. 66)

Is not this still the question? Even after Dostoevsky; even after Nietzsche?