Juggling has a very ancient history. In the very least it goes back to ancient Egypt, and it is probably as old as civilization itself. It probably doesn’t predate civilization since cavemen had no calories to spare for something like juggling.
The origins of jugglers aside, were we ever persecuted? According to “A History of Juggling” at Juggling Magic:
Jugglers went through some tough times – after the fall of the Roman Empire and the arrival of the Middle Ages, jugglers were sometimes persecuted and seen as dirty scoundrels or even thought to be witches.
“Dirty scoundrels”? Sounds like we had it really rough. Not quite like the Jews or heretics, but this does sound like bigotry that could inspire violence. However, not everyone agrees that jugglers were looked down on and persected in Europe during the Middle Ages.
According to Arthur Lewbel(2002) in “Research in Juggling History”
Another modern misconception is that medieval church considered juggling to be a black art or a tool of the devil. In fact, I have never seen any evidence that the medieval church ever specifically persecuted jugglers or juggling. If anything, the examples in Fletcher  and the appearence of jugglers in the margins of illuminated manuscripts would suggest the Church’s approval of juggling.
This directly contradicts the first quote. Indeed, the first quote cites no evidence to back its claim that jugglers were persecuted in Medievel Europe. Now it is possible that they may have been persecuted briefly in a few areas but we have no evidence of widespread, systematic persecution. If anyone ever did persecute jugglers in Europe, it probably would have been radical Calvinists or Puritans due to their very austere, artless approach to Christianity.
Since there is some overlap between court jesters and jugglers, let’s look at what jesters went through during the same time period. Though being a court jester is not the same thing as being a juggler, some jesters were jugglers. This profession fell in and out of fashion during the Middle Ages, largely dying out by the 19th century as nobles turned more toward music and imperialism for entertainment. While it fell out of fashion at times, and some jesters were jailed for telling bad or inappropriate jokes, they weren’t systematically persecuted.
When the radical Puritan military leader Oliver Cromwell overthrew and executed King Charles II and became King himself of Britain in all but title, his court has no use for jesters or jugglers, unlike previous rulers. There is no evidence he persecuted jugglers, though it was harder to be an actor or performer in Cromwell’s Britain due to the Puritans’ belief that the performing arts were inherently “sinful” and “pagan”, leading them to shut down just about all the theatres. In many ways the situation in Britain after the radical Puritan “Roundhead” takeover was similar to Iran after Khomeini took over in 1979. On the other hand, at least Cromwell allowed the Jews to return to Britain, having been expelled a few centuries ago on the orders of an anti-Semitic monarch.
I haven’t done a lot of research, but in more modern times, it doesn’t look like Nazi Germany, the Soviet Union or any other murderous, oppressive regimes persecuted jugglers. I don’t believe I’ve ever heard anything about Stalin sending jugglers off to the Gulags. As an aside, if being bigoted against jugglers was more widespread, what would these bigots be called? “Anti-jugglites”? “Anti-jugglerites”?
So no, there isn’t any reliable evidence that jugglers were persecuted. If we were, would you pity us?