In Medieval natural philosophy, the supernatural made perfect sense: things had their own natures, that caused them to act as they do. But a force greater than their nature could intervene and cause them to act otherwise. So bread naturally (per its nature) nourishes us, but a supernatural act can cause it to become the body of Christ.
However the scientific revolution did away with these "natures." There was brute matter, whose only nature was occupy space, and then there were laws imposed on this brute matter by God: in a sense, all of nature only "worked" because of divine commandment. The fact that these were divine commands to nature was why they were called laws! Attempts to explain natural phenomena by "natures" were mocked; see Moliere's parody of medieval natural philosophy where the doctoral student explains that opium causes sleep because of its "dormitive powers."
But many later scientists, under the sway of 19th-century ideologies, forgot the supernatural nature of their own laws, and came to use "supernatural" as a term of derision. But in our modern context the term is what Rand would have called a "stolen concept": any coherent idea of the supernatural is going to catch the modern "laws of nature" in its nets, and that is definitely not something the people using the term derisively want to do!