When Virginia was started as a colony, the English monarch was the head of the church as well as head of the state. Political authority and religious authority were centralized - and religious dissent was potentially treason.
James I and subsequent Stuart monarchs claimed they had the authority to govern by the "divine right of kings." In the 1530's Henry VIII had rejected the authority of the Pope in Rome, establishing himself as the head of the Anglican Church. Queen Mary later re-established Catholoicism as the state religion, but she was replaced by Queen Elizabeth I. The "virgin queen" restored Protestantism as the official religion, and all government officials had to take the Oath of Supremacy.
The English rulers insisted on one and only one official church. They did not endorse others establishing their own independent denominations. After all, independent religious movements might lead to independent political movements...
While Virginia was a colony, there was no guarantee of religious freedom. The Anglican Church was "established" as the official church of England, and Virginia was an Anglican colony - even more so when it became a royal colony in 1624 after the charter to the London Company was revoked.
After 1634, however, there were always Catholics on the Virginia border, thanks to the son of James I.
Charles I was married to a Catholic and was sympathetic to that religion. His wife, Queen Henrietta Maria, was the daughter of the the French ruler Henry IV. The marriage was arranged for political reasons, to encourage an alliance between those rival governments, but the two actually fell into love. The relationship started off with some difficulty. Charles I did not actually travel to France for the wedding; he sent a representative, which was an acceptable practice rather than a snub. However, the representative was unable to attend the ceremony in person - it was a Catholic rite, and he was a Protestant. The reverse occurred when Charles was crowned as king. Maria was unable to attend the coronation in person, since it was a Protestant ceremony and she was a Catholic.
The English Civil War resulted in Cromwell and the Puritan Army displacing Charles I in 1642 and then executing him in 1649. It was a war for power and control, exacerbated by Charles I's perceived support for Catholicism. Remember, international alliances were based on personal connnections (such as who was married to whom...) and national religions.
The sympathies of Charles I were revealed in part when he granted the charter for the colony of Maryland. This was originally intended to be a grant to George Calvert, who had served as a key official (Secreatary of State and Privy Councillor) to James I. George Calvert converted to Catholicism and resigned his official positions, but the king created the title of Baron Baltimore for him and Charles I planned to meet his request for a colonial grant.
Calvert was no starry-eyed religious zealot thinking of getting a fresh start in the New World. Starting in 1620, Calvert had sponsored a settlement known as Ferryland in Newfoundland. It acquired a reputation as a haven for Catholics fleeing England, but the colony was not an economic success. After Calvert personally visited his colony in Canada, he discovered:2
George Calvert, the first Lord Baltimore who wrote to the king asking for a new grant in Virginia, died just before Charles I issued his 1632 charter for the requested proprietary colony. The king gave the charter instead to George Calvert's son, Cecil Calvert, and requested that the new colony be named after Queen Maria. Maryland, named after a Catholic queen, was from the beginning a place where Catholics were welcome.
The settlers in Virginia did not appreciate the creation of Maryland. It gave to the Calverts valuable lands that the Virginians considered to be theirs. Most affected was William Claiborne, who had arrived in Virginia in 1621 as the colonial surveyor and established a fur trading post on Kent Island in 1631. (If you take Route 50 east of Annapolis/Baltimore to the Eastern Shore, you'll cross Kent Island on the eastern side of the Chesapeake Bay.)
Claiborne was evicted by the Calverts, and Charles I refused to grant his appeal that his pre-existing claim to the island should be exempted from the grant of "a Country hitherto uncultivated" to the Calverts. Claiborne had partial revenge - he spurred the Susquehannocks to take their fur trading business to the Swedes in Delaware, rather than do business with the Maryland colony. Claiborne's dispute with the Calverts did not end there, however. He participated in the 1644 revolt against Leonard Calvert, seizing St. Mary's City for several years. Later, from 1652-57, he served on the Parliamentary commission that governed Maryland under Cromwell - but was still unable to regain control of Kent Island.
Maryland settlement under the Calverts started with the arrival of the Ark and the Dove in March, 1634. The majority of the first settlers at St. Mary's City were Protestants, but clearly Catholicism would be accepted in the colony. The first religious service in the colony was a Catholic ceremony led by a Jesuit, Father Andrew White.
In 1649, Maryland passed the Act of Toleration in 1649, which said:
This legislation was not based on an ecumenical movement or modern perception that each religion has value. Instead, it was a political move to attract new settlers. In the 1640's, the population of Virginia and Maryland increased through immigration rather than natural births of existing colonists. Recruiting settlers from Europe to serve as indentured servants was not easy - and the Calverts recognized that they could attract dissatisfied settlers from Virginia.
The Governor of Virginia, Lord Berkeley, and the House of Burgesses did not welcome the Puritans. The Calverts encouraged them to settle in Anne Arundel County, increasing the population of their colony and stimulating more economic growth (primarily through greater tobacco exports).
Part of the strategy was to steer the Virginia Puritans to settle on the edge of their existing population centers, serving as a buffer between the existing settlements and the Susquehannocks and Iroquois raiders from the north. Virginia did the same thing a century later, welcoming the immigrants from the Palatinate - the "Pennsylvania Dutch" - to the Shenandoah Valley.
References1. "The House Of Hanover - Frederick, Prince of Wales," http://www.englishmonarchs.co.uk/hanover_8.htm (last checked October 23, 2011)
2. Letter from Sir George Calvert, Lord Baltimore to King Charles I, 19 August 1629, http://www.heritage.nf.ca/avalon/history/documents/letter_14.html#winter (last checked October 23, 2011)
statue honoring Brent family on Route 1 in Stafford County