Where the Reformers Erred in Their Doctrine of the Church
By way of reaction from the Romish error that the church must govern the state, they concluded that the state must to a large extent govern even the spiritual affairs of the church. That accounts for Article XXXVI of the Belgic Confession in its original form of 1561. And even the Westminster divines, nearly a century later, held that it is the duty of the civil magistrate “to take order, that unity and peace be preserved in the church, that the truth of God be kept pure and entire, that all blasphemies and heresies be suppressed, all corruptions and abuses in worship and discipline prevented or reformed, and all ordinances of God duly settled, administered, and observed For the better effecting whereof, he hath power to call synods, to be present at them, and to provide that whatsoever is transacted in them be according to the mind of God” (Westminster Confession of Faith, Chapter XXIII, Section III).
It was not until the eighteenth and nineteenth centuries that the Scriptural teaching of the separation of church and state gained anything like broad acceptance within Protestantism.
– R.B. Kuiper, The Glorious Body of Christ