As early as the end of the 1680s, Thomasius had blamed the corruption of faith on the self-interest of clergymen, who tried to turn religion into a pretext for pursuing their own ends. Their contrived philosophical glosses on theological questions allowed them to distort revelation and to establish their “primacy within the church and [their] control of secular power,” by pretending that their particular interpretation of scripture was based on superior expertise and represented the only true faith. Rival opinions were labeled heretical, although, Thomasius argued, it was precisely the “scholastics’ “ introduction of philosophy into religious debate that produced schisms and heresies, which eventually damaged the most important Christian virtue of all, charity. The critique of this orthodox Lutheran “priestcraft” or “papalism” remained a central part of Thomasius's thought in the following years, and it became even more prominent when his theological views changed around 1693 and Thomasius no longer believed there was any need for doctrine in Christian religion at all.

An important aim of Thomasius's criticism was to strengthen the powers of the secular ruler over his territory's church, in particular, the powers of the Calvinist prince of Brandenburg to intervene in the affairs of his territory's Lutheran congregations. Thomasius's defense of the ruler's rights is often described as secular, absolutist, and statist. It is seen as part of the emergence in the Holy Roman Empire after the 1648 Peace of Westphalia of a deconfessionalized system of sovereign territorial states. The religious plurality and toleration introduced by the peace, it is argued, meant that political power could no longer assume confessional homogeneity in a particular territory and thus could not rest on a religious basis.

The Peace of Westphalia, however, did not separate law and politics from confessional questions in principle, but produced only a multi-confessional settlement. It extended official toleration to one confession that had not enjoyed it previously under imperial law, because it had not been included in the Peace of Augsburg of 1555, that is, Calvinism.