It wasn’t just freedom to express their religion, it was also the freedom to form governments where they could be in power, and thus impose their religious beliefs on others.
The British colonies were basically religious fundamentalist zones. For example: Maryland – land of Mary. Was intended to be a Catholic colony. Massachusetts was meant as a Puritan colony, and they strictly enforced that. A woman named Mary Dyer was hanged in Boston for the crime of being a Quaker.