And who started those wars? They were doing fine until they decided to revolt and siege cities. That tends to make the local king weary of them and desiring for an inquisition to figure out who they are so they don't rise up again.
It is worth noting that these groups, which began in the 1200s or so, were not like protestantism. They are actually inspired by ideas from Manicheanism, a blending of paganism, Christianity, Gnoticism, and in some cases eastern traditions.
I am unsure as to what era or specific people you refer to, but you surely need to revise your Christian history.
The Roman church has no interest of course in admitting that Christianity spread throughout the world independently of Roman authority. The churches of Britain that existed before the time of Patrick had no connection with Rome., and it is only Roman engendered myth that has Patrick himself submitting to Roman authority. The Roman Church 'adopted' such early stalwarts of faith such as Patrick and Columba, building her own edifices on the sites of the original colleges. Patrick, Columba, Columbanus, Dinooth and Aiden were all true evangelists and helped establish a network of colleges and churches all over Britain, a long time before Rome had any real foothold there. These theological colleges and missionary schools were established completely independantly of Roman authority, one example being the famous college of Iona, from which Columba sent missionaries to Scandinavia, Holland, and Germany.
When the gospel was first introduced by Paul to the Galatians, even Paul could not have known the widespread impact his missionary ministry would have. The Galatians were of Celtic origin.Originating in Britain 3 to 4 hundred years before Christ, these fiery warriors at first settled southern France, then ventured into Italy where they decimated Rome, and finally settled in the area of Asia Minor where Paul found them. These Celtic people retained their connection with their homeland and with their own blood, regularly traveling back through the south of France to Britain for trade. For hundreds of years these Celtic people of Asia minor even spoke the same language as those in Italy and France and Britain. The Celtic influence throughout Asia was in fact so strong that Alexander the Great chose to agree to terms with them rather than risk combat.
After Paul's visits and success with the gospel, these people took the gospel with them back to Britain. The Celtic church of Britain therefore had its origins possibly before the turn of the first century, spread quickly throughout Ireland, Scotland, Wales and England, bringing peace to those who embraced it, and uniting tribes and clans that formerly were bitter enemies.
When Augustine arrived in Britain as a Roman missionary in the 4th century he was shocked to find a flourishing church already in existence there. His demands that the Celtic churches submit to Rome were roundly refused, while fellowship with Rome was respectfully accepted. Rome would have none of that of course, and political intrigue and war ensued over the centuries and continue to this day.
The same went for other independent churches such as the Waldenses. To allow a Christian church to exist within a stones throw of Rome yet not be subject to Roman authority was anathema to the Vatican and for centuries the Waldensian people were pursued, persecuted, and their books and writings destroyed to correct this anomaly on the papal doorstep. The Waldenses, named for the area in which they lived (Vallenses Valleys of Northern Italy east of the Cottian Alps around Milan), began as a small protest movement in the second century, their first leader being Helvidius, and they vigorously preached against the inroads of paganism into Christianity, particularly in Rome. Monasticism and asceticism plus the introduction of 'baptised' pagan festivals offended these simple people of the valleys but their protests went unheeded and eventually they were chased from their homes and were among the first Christians to flee into the wilderness and settle as Christian communities away from the influence of the organised church/state union developing in Rome.
I could continue to write of the churches that from the second or third centuries were established as far as China and all places in between....quite apart from any Roman influence.