What caused christendom to be a troubled realm at the end of the middle ages?

Wicked monarchs, like Henry VIII, tried (unsuccessfully) to destroy the Church, to help them achieve their own twisted ambitions. Even today some politicians are anxious to turn Britain into a pagan/humanist country. Pope Urban II , tried (unsuccessfully) to force those of other faiths to convert, to help them achieve their own twisted ambitions. Even today some priests are anxious to put all the pagans/humanists/atheists to the torch and blame them for all of Britain's ills.