If you've seen any anime of the Fate series you may have noticed a trend. With the exception of Emiya from Fate/stay night, Waver (and his students) from Lord El-Melloi II's Case Files: Rail Zeppelin Grace note, and Fujimaru from Fate/Grand Order Absolute Demonic Front: Babylonia, nearly every mage we've been introduced to is a bit of a dick at best, a mass murderer at worst. Even when they're not trying to kill each other in one Holy Grail War or another, mages are far more antagonistic than they are friendly.
Or to put it another way, they're assholes.
Now, before we start getting into this, allow me to give a little disclaimer: this is a basic look at mages and magic in Fate—key word being “basic.” I'm going to be talking in generalizations and using common nomenclature so I don't have to define every proper noun we come across.
Across the Fate franchise—and other works that are part of the Type-Moon-penned multiverse—we've seen time and again that mages, in general, seem to have no issue killing civilians and other mages alike to get what they want. The reason for this mindset is simple: Those who identify themselves as “mages” are all part of a generations-long race towards the same goal—the ability to use magic. Mage families pass on all their knowledge—their spells and theories—to their children in the form of a magic crest. In this way, each generation can build on the last without needing to relearn everything as they pursue the ability to use magic. But before we go any further, it's important to point out here the difference between magecraft—i.e, the supernatural abilities we see mages using—and true magic.
Magecraft basically bends the rules of reality to do something with a spell that is possible through non-magical means. For example, Rin's Gandr spell can shoot a person from a distance causing small, but serious, localized damage. Of course, a pistol can do the exact same thing. Magic, on the other hand, doesn't just bend the rules of reality—it shatters them. Time travel, teleportation, bringing the dead back to life: this is the realm of true magic. To put it another way, if the result is something that could conceivably be achieved through science or technology, it is magecraft. If it is something truly impossible by any means in our world, it's magic—and true magic is not exactly easily obtained.
But it wasn't always this way. In the distant past during the Age of Gods—think ancient Babylon (700 B.C.E.) and older—magic was plentiful and science was in its infancy. Literal gods walked the Earth and magical creatures were common—as were wielders of magic. At this point in time, “magecraft” and “magic” were, for all intents and purposes, the same. However, as civilizations continued to develop, magic declined as man and science began to overtake the planet. While the specifics are unknown, the general idea is that as more and more things once thought only possible by magic were achieved via science, magic became less, well, magical.
In the modern era, Magecraft is powered by the very “Mystery” surrounding it—the supernatural aspect of how it is done. If everyone knows how to do something—be it through magical or scientific methods—the magecraft loses much of its power. Mages cling to scraps of Mystery to power their magercraft, doing what they can to sustain it. They live in a secret society. The mechanics behind their spells are closely guarded family secrets, and the older and more secretive they are, the more powerful they become.
This, in turn, is why someone like Waver is both looked down upon and feared. He chairs the “Modern Magecraft” department. New magecraft lacks much Mystery and is, therefore, the least powerful type of magecraft. However, by demystifying magecraft, Waver is able to look at the magecraft of others and figure out how they work. To many, this makes Waver an anathema. He is the death of their magecraft—the very thing they have spent generations perfecting. His very existence rocks them to their cores.
Magic in the modern era, however, is a bit different. By the time of Fate/stay night, there are five true magics that exist. And among those, only three—the Second, Fourth, and Fifth—are currently claimed. Nearly all mages seek the remaining two—or a new magic all their own. Unfortunately, the First Magic can only be obtained by the people of a certain bloodline. So that's out.
The other remaining unclaimed magic, on the other hand, is absolutely up for grabs. The Third Magic, “Heaven's Feel”, is the ability to make the soul physical—even if that soul is a hero from a myth or legend. The entire Fate franchise in general is all about those fighting to gain the Third Magic, or rather, a wish-granting “magical machine” of sorts that uses the Third Magic. With something as important as the Third Magic, you'd expect that every mage under the sun would be clamoring to participate in the Holy Grail War. However, there are several reasons this is not the case. The first is because the Holy Grail War's true nature is a secret of sorts—most Western mages see it as an obscure backwards ritual not knowing its link to the Third Magic. The second is that, since it's a fight to the death, there's a good chance you'll die if you get involved and your family's crest—literal generations of magical knowledge—will be lost. Finally, the Holy Grail War isn't the only way for a mage to obtain true magic. In fact, there are potentially infinite ways.
In a world with so little Mystery left, there is only one place to get enough Mystery to fuel real magic: the source of all unexplained phenomenon in existence known as the "Root.” The Root is a metaphysical place outside of our dimension. It contains all the histories of every parallel world from the start of time to the end. It is also where souls come from and where they return to after death. Simply put, if a mage is able to divine a way to reach the Root, they are granted magic. However, there is a bit of a trick to it. Each path to the Root can be used only once so people can't use the same methods access true magic. That said, the magic that is granted from accessing the Root can be passed on to another person in various ways. And moreover, like we see with Heaven's Feel, magic, once discovered, is never truly lost—even if no one inherits it.
By their very nature, all mages are trying to get to the Root. This is the main goal of not only their lives but of the lives of every generation of their families—past and future—as well. And all this brings us back to the reason why the mages in Fate are such assholes. To be a mage, you must have the bottomless ego and pride to believe you (or those who come after you) will do what only five people before you have: discover true magic. Moreover, you have to believe that you are superior to all other current mages and their families—that your family's history and research will allow you to reach the root before all others. They're basically all fanatical, egotistical psychopaths. Killing civilians? Using other mages as batteries for your experiments? If it gets you to the Root and true magic, who the hell cares about things like morality?
However, they're not completely without sense. While they do have serious tunnel vision, the wiser among them know that if magecraft is thrown around willy-nilly, not only could it cause a war between normal people and mages, it could also destroy the last vestiges of Mystery that are powering magecraft by bringing magecraft out into the open. And if that happens, no one reaches the Root ever again. The Mages Association basically serves as a check and balance to the mage community in two ways. The first is basic punishment: the promise to hunt down any mage who endangers magical society at large. The second is prevention. When young mages come to the Clocktower to get an education in magecraft from its numerous masters (a tempting offer that even ancient mage families can't resist), they are also indoctrinated with the rules they need to follow.
And while it's true that many mages bend these rules (or break them on the down-low) in their attempts to reach the Root, the fact that mage society hasn't been exposed proves the system is working—well, at least as well as can be expected amongst a group of narcissistic, obsessed zealots. Is it any wonder that Emiya, Fujimaru, Waver and his students are the only sane and moral people in this crazy, magecraft-filled world?