From what I understand, the former English colonies in 1787 had effectively no non-Protestant population. There were some old Catholic families in Maryland, a few thousand Catholic Irishmen across the country, and very tiny Sephardi Jewish communities in certain coastal cities. Although some individual colonies were founded by certain groups to protect their ability to worship freely, the religious history of the English colonies was generally antagonistic and sometimes violent. In the 1650s, Puritans banned Catholicism from Maryland, despite that colony's Catholic origin. Around this same time, Jews were expelled from Georgia.
The religious protections of the first amendment have had pretty huge implications on American law, history, and demographics. But why was it written? I'm surprised that the religious conservatives who dominated colonies like Massachusetts let this amendment be ratified. Were there fears that religious freedom would compromise the colonies' Protestant character? What kind of backlash did this amendment instigate?
While you are waiting for an answer you can take a look at this book The Founding Fathers and the Place of Religion in America by Frank Lambert. Its great and will clear up a lot of your misconceptions.