The church considered the magical philosophy a "threat to Christian faith" for several reasons.
The first was that, by boast or reputation, magicians were supposed to be able to accomplish feats comparable to the miracles of Jesus. Indeed, Trithemius reported that the historical Faust was claiming that "the miracles of Christ the Savior were not so wonderful, that he himself could do all the things that Christ had done, as often and whenever he wished." Since the miracles of Jesus were offered as proof of his divinity and of the truth of the gospels, the similar miraculous accomplishments of the magicians were supposed to undermine Christian faith. Perhaps Jesus was not the son of God, but just a clever magician…
Another reason that the church attacked the magical philosophy was the danger of demonic magic. First there was the risk that one might accidentally contact a demon rather than an angelic spirit, or that the Devil might deceive one into doing so, and thus a well-meaning magician might inadvertently do evil; even practitioners of spiritual magic acknowledged this danger and took precautions to avoid it. Further, natural magic was inherently dangerous, since it involved commerce with elemental and planetary, rather than angelic, spirits, and therefore was tainted with imperfections of matter. It was not even conceded that God permitted humans to engage in angelic magic.
The second problem was the temptation to do diabolical magic willingly, to sell one's soul to the Devil. Against this possibility, the story of Faust was offered as a cautionary tale. (Indeed Agrippa had the reputation of being a black magician, although his writings do not support that opinion.) Thus it was argued that any effective magic must be Satanic, because the last genuine miracle was the Resurrection; since it had established the truth of the Christian religion, no further miracles were necessary, and God did not allow them. Thus the church purged itself of all magic (although the apparent "magic" of transubstantiation and religious relics posed continuing problems). The natural world was devoid of occult properties.