This is also true of sorcerers, who have innate magical talent. Even standard wizards tend to do it, even though sorcerers can cast more spells per day than them.
Warlocks suffer an even worse treatment (due to their powers often but not always having a demonic origin) and Complete Arcane (the book introducing the class) points out how it should be standard for most settings to scorn, resent, and persecute warlocks. Given that warlocks are casters who have an unlimited store of spells (unlike the sorcerer, who will eventually run dry), and probably made a Deal with the Devil to get their powers (which, by the way, are far more focused on killing people than those of Wizards or Sorcerers), this really makes no sense.
There are also half-dragons, who are almost always treated badly by humans in Dungeons & Dragons. Yes, they think it's a good idea to pick on the person with claws and sharp teeth who can breathe dangerous substances and who has a parent that can level the town, and often will do so to protect or avenge his/her child. Eberron averts this by making the half-dragons considered abominations by the dragons. Furthermore, even in the core game a lot of dragons are lax parents even with their pureblood children and are even worse towards their half-breed spawn, making this kind of justifiable — there's no guarantee that their dragon parent will care — but not quite.
The Dragonblooded supplement has a short story at the beginning of the chapter on Spellscales in which the main character encounters a young spellscale girl being bullied by a mob of normal kids, and managing to cast a high-enough-level Sleep spell to knock out eight or ten at once.
Wizards and Psykers of Warhammer and Warhammer 40,000 respectively. The Wizards normally don't give a damn about what peasants think but soldiers love them, and psykers, well, their powers come from Chaos... Considering that psykers are incredibly vulnerable to Power Incontinence, Demonic Possession, and in more than a few occasions having their skull turned into a portal to allow The Legions of Hell to overrun the planet, this trope becomes even more ridiculous if treatment of them within the Imperium wasn't less "ostracism" and more "immediate execution."
In the Deathwatch supplement Honour the Chapter, The Black Templars' history in the Jericho Reach began with a Prelate-Imperialis named Nadab Saul trying to convince the Black Templars to join the nascent Achilus Crusade in the worst ways possible. He tried to browbeat and intimidate the Marshals instead of appealing to their sense of duty. Even as Battle-Brothers hauled him away, never to be seen again, he continued to spit invectives, condemning the entire Chapter as traitors.
The Elder Land Wurm's flavor text: "Sometimes it's best to let sleeping dragons lie."
Played with via the card Slumbering Dragon, which can't attack or block until it's had several counters put onto it. It gets counters whenever something tries to attack its controller.
In Pathfinder, this mentality is actually something that hags seek in villages to foster their changeling offspring. See, changelings are essentially Cute Monster Girls who more or less fit the anime Cute Witch look. Hags need to perform a magical ritual in order to transform them into the hideously ugly and more powerful hag forms — but they can only do so if the changeling accepts the ritual. As a result, the hags strive to ensure that the families or villages they foster their spawn to will be sufficiently hostile to someone who isn't "normal" that, when the hag makes the offer to her daughter, the embittered changeling will gladly accept in hopes of using that power for revenge. Needless to say, when the new hag has been reborn, she usually pays back her tormentors in spades.