The very notion of tolerance, of “live and let live,” was almost nonexistent in early-modern Europe. Exceptions did exist, especially in the Holy Roman Empire, but beliefs clearly hardened over the course of the sixteenth century: what tolerance had existed in the early decades of the Reformation era tended to fade away.
This was not just about Catholic intolerance; while the Catholic Inquisition is an iconic institution in the history of persecution, most Protestants were equally hostile to Catholics. This was especially true among Huguenots in France, who aggressively proselytized and who imposed harsh social and, if they could, legal controls of behavior in their areas of influence, which included various towns in southern France, not just Switzerland. In addition, while actual wars between Protestant sects were rare (the English Civil War of the sixteenth century being something of an exception), different Protestant groups usually detested one another.
Why was religion so divisive? It was more than just incompatible belief-systems, with some of the reasons being very specific to the early modern period. First, religion was “owned” by princes. A given territory’s religion was deeply connected to the faith of its leader. Princes often held some authority in church lands, and priests had always served as important royal officials. There were also numerous ecclesiastical territories, especially in the Holy Roman Empire, that were wholly controlled by “princes of the church.” Likewise, only states had the resources to reform whole institutions, replacing seminaries, universities, libraries, and so on with new material in the case of Protestant states. This necessitated an even closer relationship between church and state. In turn, an individual’s religious confession was concomitant with loyalty or disloyalty to her prince - someone following a rival branch of Christianity was, from the perspective of a ruler, not just a religious dissenter, but a political rebel.
At the same time, over the course of the sixteenth century, specific, hardened doctrines of belief were nailed down by the competing confessions. The Lutherans published a specific creed defining Lutheran beliefs known as the Augsburg Confession in 1530, and the Catholic Council of Trent in the following decades defined exactly what Catholic doctrine consisted of. There was thus a hardening of beliefs as ambiguities and points of common agreement were eliminated. With all sides holding to their own.