The term stems from the great witch hunts of the Renaissance—one of the less enlightened activities of that time period—and references in fiction often mention the infamous Salem Witch Trials, although similar hunts were going on throughout Europe during the same era. England had officially-appointed witch-hunters going from town to town. Paid for every witch they caught, they were highly motivated to find what they were looking for, though the hunts in England tended to be less severe than their mainland European counterparts. On mainland Europe, various inquisitions, including The Spanish Inquisition, were searching out witchcraft as well as heresy, and extracting confessions of witchcraft under torture was a popular way of making unpopular people disappear. The worst of the witch hunts occurred in the Holy Roman Empire. Modern-day historians have pointed to several reasons for this: One of the more popular explanations was the lack of central authority in the Holy Roman Empire and remote regions of modern-day France. This led to a lack of oversight and allowed for powerful individuals to instigate hundreds of trials. Modern historians estimate roughly fifty thousand people, disproportionately though not exclusively women, were executed in the European witch hunts.
Many people assume that literal witch hunts are a thing of the past, but they are still found in many parts of the third world. Nor are they purely limited to so-called "primitive" cultures. In the "Satanic Panic" of the seventies, eighties, and nineties, fears of modern Satanism in the US and UK, fueled by popular pseudo-scientific exposés (like Mike Warnke's infamous book The Satan Seller) and backed by since-thoroughly-discredited hypnotic techniques to recover "repressed" memories, led to many people being convicted of witchcraft-inspired murder and abuse. People were convicted with the flimsiest of evidence, and some of them are still in prison today.
Still, despite the occasional literal witch-hunt, in the modern era, figurative witch hunts are far more common, and generally involve politics or political positions. The '50s-era Red Scare, led by Senator Joseph McCarthy and the House Un-American Activities Committee (HUAC), asked many people, "are you now or have you ever been a Communist?" Coming to your senses and repenting your youthful folly was not considered a sufficient excuse, since you might be pretending. Again, people were convicted on the flimsiest of evidence, and both communists (and former communists) and the falsely accused had their lives ruined by the HUAC. Today, in America, the term "McCarthyism" is synonymous with political fearmongering. Arthur Miller's play, The Crucible, was written in response to McCarthy's activities, and it recast the Red Scare as a literal witch hunt.
Throughout the world, political witch hunts have been a popular way of enforcing political correctness, and eliminating those with unpopular opinions. The Stalinist purges in Soviet Russia eliminated millions suspected of not toeing the official USSR Communist Party line. Kids were encouraged to report their parents to the secret police. Similarly, China had the Landlord Purges after Mao came to power. In Nazi Germany, it used to be said that the Gestapo had a spy on every corner looking for anyone who might be a threat to the Reich. Actually, the civilians would use the Gestapo to settle old scores. During the Occupation of Paris, French citizens routinely used the Gestapo to eliminate rivals.
In speculative fiction, mutants are a popular target for witch hunts. Being a mutant is a nice, generic way of being an outsider that makes it easy for real outsiders of all types to identify with. A.E. van Vogt's 1940 novel, Slan became an instant hit among nerdy science fiction fans for just this reason. Other popular victims of futuristic witch hunts include scientists and Transhumanists. Contrariwise, in works depicting repressive futuristic theocracies, it's common for the rebels to identify with, and even pretend to be, actual witches, as first seen in Robert A. Heinlein's novella, "If This Goes On—".
