It was manifestly not merely a coincidence that Lord Baltimore appointed a Protestant governor, William Stone, and commended to the Maryland Assembly, in 1649, the enacting of "an Act concerning Religion," drawn upon the lines of the Ordinance of Toleration adopted by the Puritan House of Commons at the height of its authority, in 1647.[59:2] How potent was the influence of this transplanted Nansemond church is largely shown in the eventful civil history of the colony.

When, in 1655, the lord proprietor's governor was so imprudent as to set an armed force in the field, under the colors of Lord Baltimore, in opposition to the parliamentary commissioners, it was the planters of the Severn who marched under the flag of the commonwealth of England, and put them to rout, and executed some of their leaders for treason.

When at last articles of agreement were signed between the commissioners and Lord Baltimore, one of the conditions exacted from his lordship was a pledge that he would never consent to the repeal of the Act of Toleration adopted in 1649 under the influence of the Puritan colony and its pastor, Thomas Harrison.
In the turbulence of the colony during and after the civil wars of England, there becomes more and more manifest a growing spirit of fanaticism, especially in the form of antipopery crusading.

While Jacobite intrigues or wars with France were in progress it was easy for demagogues to cast upon the Catholics the suspicion of disloyalty and of complicity with the public enemy.

The numerical unimportance of the Catholics of Maryland was insufficient to guard them from such suspicions; for it had soon become obvious that the colony of the Catholic lord was to be anything but a Catholic colony.