Why were religious dissenters so frequently persecuted in late-sixteenth-century and early-seventeenth-century european nations like england?

Religion, at that time, was governed by the State. In such, the government controlled all aspects of religious life and what sorts of materials would pass muster as being "proper" and what viewpoints would be considered "non-threatening" to the health of the nation. Any belief systems that were outside of this were considered verboten.