Descartes is writing in the 1630s-40s. Witch trials are at or near their peak in this period. The great witch panic is fundamentally an early modern phenomenon, not a medieval one. The Thirty Years War, which is happening while Descartes is writing his rationalist program, is a conflict of almost incomprehensible sectarian savagery. Newton, thirty years later, writes more on biblical prophecy and alchemy than on physics. Kepler's mother was tried for witchcraft. The same period that produces the Scientific Revolution produces the most intense witch persecution in European history, produces the Rosicrucian panic, produces the full flowering of ceremonial magic as a literate, intellectually serious pursuit.

This is the thing that the standard Enlightenment narrative totally obscures. The so-called Scientific Revolution didn't replace magical thinking among educated Europeans. It existed in parallel with it, often in the same people, for at least another century. The split between what we'd call science and what we'd call occultism only hardens in the 18th century, and even then it's messier than the textbook admits.

(http://www.autoadmit.com/thread.php?thread_id=5856241&forum_id=2...id.#49811798)