“(John) Locke was a Christian and his arguments reflected the temper of his times: expressions of piety and references to the importance of salvation abound. But if one removes these elements, his arguments for toleration and keeping the state out of religious affairs could be made just as easily today. His key insight is recognizing that governments have no theological competence; they need to concern themselves with this-worldly matters.
In assessing Locke’s arguments for toleration, it is important to note the connections between these arguments and his social contract theory, including his claim that there are certain natural rights. The strength of his arguments for toleration depend, to a large extent, on acceptance of both his contention that the natural state for humans is one of freedom and equality and his contention that the consent of the governed is the only legitimate way in which governments can acquire power. If one rejects these contentions, the first two arguments for toleration lose much of their force. For example, someone committed to the view that a government’s legitimacy is based on the grace of God may dismiss the importance of the consent of the governed. Who cares what the people want? It is what God wants that counts. Moreover, Locke’s second argument implicitly relies on his claim that individuals have a right to freedom of conscience. It is true that coercion of an individual cannot compel genuine belief by that individual. However, one must remember that the justification offered for religious persecutions was not so much that they helped to save the individual heretic- the person with erroneous beliefs- but rather that they helped those who might otherwise be contaminated with false religious beliefs. Thus, a thoroughgoing theocrat would be unmoved by Locke’s arguments for toleration. The salvation of the many takes precedence over any purported right of the individual. ”
–Ron Lindsey, The Necessity of Secularism, pgs 29-30