Or, if there are rules, it isn't magic, and why that matters
Mastery of a subject is not without some intrinsic virtue, or at least not to those with master's degrees. Having never gone to college, I'm not sure if I personally would be a fan of virtuous power through academics.
As a young convert, I once set out to write a blog post on (pardon the terms) Catholic magic and Protestant magic. The matter is more complicated than that, of course, and now that Catholicism is no longer shiny and new I can see more subtle distinctions.
But the original distinction is that Protestantism reduces things to systems, whereas Catholicism functions on symbols. So in the Protestant fantasy, even from those who are no longer officially Protestant, the magic can be reduced to its component parts. Compare to Tolkien, where, say, the One Ring is a symbol, recalling Plato's anarchic fear of an invisible man.
I don't think this loss was intentional, and by the efforts of many writers to somehow bring the magic back, not desired even today. Jack Vance wrote a world where magic was powerful, arbitrary, and very dangerous; his heirs in D&D reduced all that to logistics. Such is engineering.
I think there is room for those writing the more mythic magics to make a comeback, since the absence of myth is so keenly felt. In my C&D series, a LitRPG, I tried adding back some of the uncontrolled symbolic aspects of the myths that had lost the original power, and my audience loved it.
But in defense of Promethean fantasy, it is not intrisically wrong to steal fire from the gods if the gods have been unjustly keeping it from the mortals. Indeed, the question is the same as in comic books: if you have the power, can you use it justly, as compared to the villains, who do not? Literature demands the villian is more powerful than the hero, although whether this state of affairs lasts is up to the author.
But to return to my original distinction, there are more things in Heaven and Earth than are dreamt of in such a division. Brandon Sanderson, a Mormon, writes the most systematic systems, but frequently it is the weaklings who win. Japanese fiction is still pagan, at least for the moment--the Death Note follows an elaborate system of rules, yet it is as much a cautionary tale about the pursuit of power as any pagan myth. And I often find myself straddling the lines.
Interesting discussion. I admit I'm not very familiar with "fantasy" literature beyond Tolkein, so I can't really comment on those magical systems. But I think, despite our best efforts, rules are hard to apply to the supernatural generally, which is probably where much of the anxiety around religious behavior comes from: how should we conduct ourselves in order to not provoke these unpredictable and chaotic unseen forces (or maybe gain their favor)? Fairy stories highlight the mysteriousness and danger associated with capricious supernatural powers, which humans aren't meant to meddle with (the occult version of learning not to touch hot stoves.) Once a vague understanding of those forces and that behavior has been achieved, though, there have always been attempts to gain some control over the chaos with magic (cooking on hot stoves), whether to make the crops grow, cure illness, or give a neighbor the evil eye. Supernatural means to supernatural ends...
Though it's not quite the same kind of magic you're referring to here (story magic is often a different animal than what people practiced in real life), I always liked this perspective on magic vs science from an anthropological perspective:
"The fatal flaw of magic lies not in its general assumption of a sequence of events determined by law, but in its total misconception of the nature of the particular laws which govern that sequence. If we analyse the various cases of sympathetic magic which have been passed in review in the preceding pages, and which may be taken as fair samples of the bulk, we shall find, as I have already indicated, that they are all mistaken applications of one or other of two great fundamental laws of thought, namely, the association of ideas by similarity and the association of ideas by contiguity in space or time. A mistaken association of similar ideas produces homoeopathic or imitative magic: a mistaken association of contiguous ideas produces contagious magic. The principles of association are excellent in themselves, and indeed absolutely essential to the working of the human mind. Legitimately applied they yield science; illegitimately applied they yield magic, the bastard sister of science. It is therefore a truism, almost a tautology, to say that all magic is necessarily false and barren; for were it ever to become true and fruitful, it would no longer be magic but science. From the earliest times man has been engaged in a search for general rules whereby to turn the order of natural phenomena to his own advantage, and in the long search he has scraped together a great hoard of such maxims, some of them golden and some of them mere dross. The true or golden rules constitute the body of applied science which we call the arts; the false are magic."
-James George Frasier, The Golden Bough