Anabaptists in the 16th century were persecuted by both Protestants and Catholics. In 1529, at the Diet of Speyer, the Anabaptist Mandate reanimated the old Codex Justinianus, which declared that anyone who rejected infant baptism would be put to death. Was it the doctrine that was so taboo? Or was it the activities of the people who believed it which tainted the doctrine by association?
Most of this is taken from Reformation Europe by G.R Elton:
So, once Zwingli initiated reforms in Zurich, the Anabaptists seem to have appeared quite soon after. Based on the ideas Conrad Grebel, the Anabaptists believed that only an adult (not a child) could surrender their sinful nature and choose Christ.
They elected their own pastors and since they were already "saved" and perceived themselves to be saints on earth, they were no longer required to follow laws or magistrates. To the Anabaptists, the secular law makers were 'God's government for sinners'.
They were to have nothing to do with civil government (what they called the sword), must not bear arms, swear oaths, carry out the duties of citizens or take part in government. They were not to obey civil dictates, but as they were saved they must follow the teachings of Christ and not get drunk and orgy up all over Switzerland.
The end result was a group of extremists who believed that the civil government was not required. This of course put the wind up everyone in a position of power as it sounded terrifyingly close to free will. I guess it was no surprise that everyone and their vicars went after them.
Allow me to remind everyone that Dan Carlin is not an accepted source in this subreddit and any links to his podcasts or any answers using him as a base for an answer will be deleted on sight.
So, first off, we can't look at Anabaptists over the 16th c. as one cohesive unit- or even argue that the movement stemmed from one genesis point. There were numerous different groups that sprung up in different geographic areas. This theory for the multiplicity of origins in the movement is termed "polygenesis."
Because of the variety that existed in the movement, we get confusion, and hatred being attributed to all Anabaptists because of the practices of certain groups (ie what went down in Münster in 1534). So the Münster indecent occurred, when a group of Anabaptists, convinced that the end times had come chose to use violence to establish the new Jerusalem on earth. Led by Jan Matthys (from Haarlem in Holland) and Jan van Leyden, they baptized people by force, they adopted polygamy, and began killing anyone who resisted. They drove all non-Anabaptists from the city and started a bloody and brutal rule.
The leaders of the movement declared that Christ's Kingdom had come, and many Anabaptists from other areas came to the city in hope- but, the Catholics in the area would have none of this violent-polygamous nonsense. They besieged Munster. Evenetually, the Catholic forces crushed the city and its resistance. Mattys and van Leyden were captured. They were tortured and executed, and their bodies were hung in iron cages--- which were toured across the country- to show all other Anabaptists who may have had the idea to start their own New Jerusalem what failing would entail. It was also to spread the message of how dangerous these Anabaptists "really" were.
These iron cages were then hung St. Lambert's church in Münster (you can see recreations of them still there today).
So this event scared the crap out of local rulers- not only could Anabaptists be religiously deviant- but they could also be politically deviant. These ones at Munster went so far as to try and begin their own city-state. This resulted in a lot of violent backlash against Anabaptists (who had already been getting it for being religiously deviant).
Other Anabaptist leaders immediately condemned the actions of the Munster Anabaptists- it was around this time that leaders like Menno Simons (from whom Mennonites get their name) started stressing that the Münsterites did not follow true Anabaptist ideals- like love, peace, separation of church and state, etc. The movement began to solidify in the mid 16th c., and Munster was cited as a deviant group- a mistake, not in line with real Anabaptist ideals.
But- even the more peaceable Anabaptists suffered because of assocation with Münster.
For non-Münster Anabaptists, the stress on separation of church and state is what got them into trouble as well. They were believed to be seditious, and it was thought they could not be loyal/proper citizens because of it.
I hope that helped! TLDR; People hated them because of the Münster incident in 1534 gave Anabaptists a bad name all over, and belief in separation of church/state made rulers believe them to be seditious. Also propaganda helped with the hate/fear mongering.
Please don't forget, simple religious unorthodoxy had been enough to get people tortured/killed/hunted for a long time in Europe before the Anabaptists. In the grand scheme of things... sadly not all that surprising.
Sources: C. Arnold Snyder. Anabaptist History and Theology. Pandora Press, Kitchener ON, 1997.
Harry Loewen and Steven Nolt with Carol Duerksen and Elwood Yoder. Through Fire & Water: An Overview of Mennonite History. Herald Press; Waterloo, 1996.
Just posting a reminder that every answer that does not provide a clear answer to the question (why they were so prosecuted) will be deleted, including posts that just summarize anabaptist beliefs or practices, or are just descriptions of particular events.
Secondary question, did the extremist antics of the anabaptists lead to their hatred or did the hatred lead to the extremism? i.e., what was the progression over time