In his tract Areopagitica Milton said that, rather than be satisfied with the formulas of Luther or Calvin, the English had to forge a new liberal version of Protestantism: “God is decreeing to begin some new and great period in his Church, even to the reforming of Reformation itself. What does he then but reveal himself to his servants, and as his manner is, first to his Englishmen?”
Simultaneously opposing the religious authoritarianism of both “High” and “Low”, Milton urged toleration and the co-existence of different forms of Protestantism. He persuaded Cromwell to show leniency to sects many saw as heretical: “Woe to us, while, thinking thus to defend the gospel, we are found the persecutors.”
He kept pushing for the full separation of Church and State, but was not anti-religion: Milton wanted a secular state on Christian grounds ”” only in such a State could a free Christian culture thrive. Imagine a new sort of Christian culture, Milton said, in which there is no priestly power, no uniformity of worship, no “orthodoxy”, just the free pursuit of Christian truth. Christianity must not stand against the spirit of liberty, but embrace it absolutely.
Interesting – Milton was still in favor of proscribing the rights of Catholics (speech, gun ownership), and also favored regulation of publishing… Most of his free speech arguments were aimed at attacking prior restraint, ie, the prohibition of the publication of a book. He still favored very aggressive libel laws (much stricter than what most of us would consider “free” speech), and saw a role for government censorship (he had acted as a censor, and argued strongly for all books being labeled with both author and printer so that multiple parties could be sought in case of libel, slander, or blasphemy).