In the passage last quoted it is clearly seen that this is the ultimate scope.

It is a reflection on Cromwell, almost by name, for not having freed himself from the notion that the settlement of Religion is an affair of the Civil Magistrate, but on the contrary having made such a supposed settlement of Religion one of the passions of his Protectorate.

It is a reflection on him, and on Owen, Thomas Goodwin, and all his ecclesiastical advisers and assessors, Independent or Presbyterian, for having busied themselves in maintaining and re-shaping any State-Church, on however broad a basis, and so having perpetuated the old distinction between Establishment and Dissent, Orthodoxy and Heresy, instead of abolishing that distinction utterly, and leaving all varieties of Christianity, equally unstamped and unfavoured, to organize themselves as they best could on the principle of voluntary association.

For the future, statesmen and ministers are invited to cease from persevering in this delusion of the great and good Cromwell.
The tract was addressed, as we have said, to the Parliament of Cromwell's son.

The preface, signed with Milton's name in full, is a recommendation of the doctrine to that body in particular.