Witch-Hunters are a popular antagonist in many media, based on a very real phenomena in the past the modern take on Witch-Hunters can vary from delusional fanatics who persecute the occult or "heretics" to outright evil, corrupt men and women of the clergy who use the superstitions of old to enforce political and social changes for their own benefits.
Often Witch-Hunters are of high social rank and thus a protagonist can have great trouble in stopping their misdeeds, in medieval societies (or similar) a Witch-Hunter may be all but untouchable by anything short of a life-threatening revolt and may have the blessing or protection of a nation, religious body or (sometimes) a mad or actively "evil" God.
In more modern settings however Witch-Hunters are often the opposite and are solitary, eccentric individuals who are at odds with society as a whole and seen as mad, dangerous or just plain foolish by everyone save those they endanger.
A heroic take on this stock character would be the Slayer (named after the famous Buffy / Angel series), who combats the supernatural and/or heretical but does so in a manner that is less oppressive and cruel : indeed some Slayers will fight Witch-Hunters due to the core differences in their philosophies or can slip into becoming a Witch-Hunter due to the phenomena of "He Who Hunts Monsters".
these are Witch-Hunters from medieval settings, fantasy or sometimes early mordern (such as the infamous Salem trails) - they are often backed by their society and thus hard for heroes to combat, they also tend to be the most corrupt or delusional.
these are Witch-Hunters from the modern (or future) era - common in comic books or films dealing with science fantasy or supernatural elements they tend to be much less accepted by society and loners by nature, they tend to be less corrupt but still very much deluded (unless they have another reason, such as vengeance or religious intolerance)
these are not strictly Witch-Hunters but fall under a similar aim of oppressing a minority (such as the occult or "heretics") - examples are evil priests, corrupt paladins and unholy knights that further senseless crusades or purges, usually for their own personal goal or delusion.