Maryland's name honors Queen Henrietta Maria (1609-1669), wife of Charles I and his second wife, Marie de Medici (1573-1642), not the Virgin Mary. The flag is from the coat of arms of Lord Baltimore and his maternal family the Crosslands.
Lord Baltimore was Catholic, and Maryland enshrined religious tolerance into colonial law for Christians who believed in the Trinity which protected Catholics as well as Christians whose beliefs did not conform to the Church of England. As a result, Cathlocism flourished in Marylad along with Protestantism. Interestingly, Catholics and Protestants, lead by William Stone the Protestant Governor of Maryland, united to put down Puritan revolt and reestablished the tolerance law following the Puritans outlawing the Catholic and Anglican faiths.