This is something you need to take back to the Roman era, when the first real preachers came to England after having converted some of the Roman armies and families. When arriving in England they realised that the current tribes/families here were so deeply rooted in their 'pagan' beliefs, beliefs that were in tune with nature and used nature and her ways, that the people would never accept a religion that based it's belief system on a human shaped person that is all powerful and the concept of 'original sin'. So they adapted, in a sense. Some smart chicken came up with the idea of 'merging' the two religions together but in a way that benefitted Christians - so for instance, they adopted pagan celebrations like Oester (Easter), Yule (eventually became Christmas) and All Hallow's Eve (Halloween). They picked up on the pagan's main god Pan, who is the half man half goat male part of the male/female creating force and also a forest dwelling god, who was celebrated for his sexuality, kindness, a father figure for nature if you will. Christians, finding the concept of a sexual god so horrific, turn Pan into Satan, a melevolant force who used sex to lure people and turn them into sinners. Armed with this 'common knowledge' they stormed England in force, preaching and turning pagans against each other as they span lies to get more people to believe in their own god.
So, by the middle ages paganism was an 'underground' religion - the people who still remembered the old ways and worshipped nature as their ancestors had done were forced to do so in secret, meeting in barns, houses, woodlands (remember, at this time and before England was mostly woodland) - anywhere secret where they could worship in peace. However should they be caught, then there was no retribution - the only route was torture and death.
So now you have a background history, i'll go onto just why pagans were persectuted. At the time of the Christians attempting to convert England (and all Romans) into a Christian society, was the time when the Romans were trying to dominate England. The two went hand in hand - religion is power and power is dominance, and with dominance you can do anything. So by crushing any previous belief systems and making people follow your own faiths, you in essence automatically become a more dominant and ruling power over those people, because they rely on you to give them sermons, read them teachings (of course, the bible wouldn't have been legible for tribespeople whodidn't understand the language) and explain how to be good Christians. In this way the Angle tribes fell to the Romans as more and more Romans took towns in the name of God.
This is about power, and about loosing it. Since the Church became so powerful and with so many followers, the fear has always been present of loosing that dominance. It wouldn't be hard for a pagan uprising to take over England again and 'ruin' all that good work, and that fear of the persecution coming back on them is too hard to bear. Also, these people lived in a time when nature and science wasn't well understood - witchcraft was attributed to such things as eclipses, bad weather, ships lost at sea, disease, infertility, colds, hair loss, animal attacks and many more. Because there was so little evidence of anything it was easier to attribute these things to someone in the village who, perhaps didn't quite fit in, or maybe was a little weird, or looked odd, than to actually spend lots of time trying to comprehend what had happened. Fear does strange things to people, and in this case it made people very irrational.
The most woeful thing, i think, is that the majority of people who were persicuted were NOT pagans - they were simple people who were unfortunate enough to get caught up in a lack of knowledge and a war for religious dominance. This isn't the only time persection like this had happened with Christians - look at the Crusades - a religous war to fend off Muslim belief and take lands that didn't belong to them, in the name of their God.
So i guess to sum up - fear, greed, and a need for power drove people to kill their fellow villagers in the name of God, or to kill people of olther religions in the name of God. I'm sure, had there not been laws today prohibiting that kind of behaviour, it would still be going on. As someone said - people will always fear that which they cannot understand, it's just what you do with that fear that makes all the difference.
Today there is not so much persecution as misinformation, People always fear what they dont know about.
Good luck on your Path.
Blessed Be)O(