To many North American Immigrants, religion was central to their entire belief system. Some sought religious freedom for their religion and an end to their persecution. In 1620, Plymouth's Pilgrims who had faced no religious persecution in the Netherlands left, as they feared their youth would be led astray. Massachusetts Bay Puritans banished dissenters to their own colonial Congregationalist denomination, banished other denominations and executed those who violated such banishment.. Catholic Maryland was a haven but soon had a Protestant majority and a virtual civil war between the two. See Turning Points in American History: The Colonial Period.

The Religious toleration process began with Puritan dissenter Roger Williams. He founded Rhode Island where he established separation of church and state and opposed forced worship. Dutch New Amsterdam allowed the first Jewish community. It  was passed by a Protestant legislature. Soon  Pennsylvania's most tolerant Quakers joined assisted the process. The English 1640's Civil Wars, which  establishment of a Puritan dictatorship, illustrated the problems of religious and political conflict.

Maryland’s famous 1649 Religious Toleration Act  protected Catholics from Protestant antagonism. The Act allowed freedom of worship for Maryland's  Trinitarian Christians, but sentenced to death anyone who denied the divinity of Jesus. It was revoked in 1654 by 
William Claiborne, a Virginian who had been appointed as a commissioner by Oliver Cromwell. He was an Anglican, a Puritan sympathizer, an Anglican and strongly hostile to the Catholic Religion.
When Lord Calvert's followers regained control of Maryland, the Act was reinstated, before being repealed permanently in 1692 following the events of the Glorious Revolution, and the Protestant Revolution in Maryland. As the first law on religious tolerance in the British North America, it influenced related laws in other colonies and portions of it were echoed in the writing of the First Amendment to the United States Constitution, which enshrined religious freedom in American law.

Why Do We Believe the Myth concerning freedom of religion. Anachronistic tendency confuse colonial practice with the 1791 First Amendment to the Constitution which banned any state established religion, established federal legal religious toleration. It did not represent  events that occurred 150 years of history and banned only Congress from establishing a state religion. State churches  continued into the 19th century. It took the 1868 Fourteenth Amendment in 1868 and 20th century Supreme Court decisions to complete the legal part of the process. Projection of events from 1791–1833 onto the 1600s is more anachronistic. Projecting our contemporary values onto the past  is more anachronistic. Because Roger Williams called  for tolerance and the separation of church and state to protect his true church from the corruption of the state is one isolated event. Turning Points in American History: 1973_Finally Brings Fast Track Civil Rights

Plenty of religious prejudice existed during all of U.S. history. Deep anti-Catholicism prejudice reached a peak in 1850 with the anti-Catholic, xenophobic,  immigration hostile Know Nothing Party