Some note that Williams never affiliated with what one would call a Baptist church. Admiration for Williams springs from his insistence on the spiritual sovereignty of the individual and his insistence on the separation of church and state.
The question of the relationship of church and state becomes clearer if one understands that while the beliefs of the first colonial New Englanders were similar there was an important difference: some were what are called Separatists, and some were not. The Pilgrims of Plymouth were Separatists. They had first journeyed to Holland and then they came to the Massachusetts when it seemed that their grandchildren would inevitably become members of the Dutch Reformed Church. They came to Massachusetts without any intention of returning to Great Britain.
The Puritans of Massachusetts Bay were not Separatists. They came to New England to be an example to the world. They believed that things in Britain would eventually go their way and that they would return to take up positions of leadership in both political and religious affairs.
The Puritans believed that the purpose of government was to help people lead a good life. Hence Roger Williams was TROUBLE. Williams rejected state-sponsored religion. This was what existed in Great Britain where the monarch was head of both the state and church. A portion of the colonial tax money went to the support of the churches and the ministers. There were also laws that required compulsory church attendance. You where you were if you had skipped Sunday services. Full church membership was also tied to voting rights.
Williams argued that there should be no official state religion. There should be no state support for the churches and the ministers. Williams also opposed compulsory church attendance. He cited the parable of the weeds and the wheat. Why should the good and the bad be forced to associate with one another if they didn't want to? Where was free will and the primacy of the individual's relationship with God?
A final piece of Williams' troublemaking was his view of the Indians. To Williams the founders of Massachusetts had clearly cheated the Indians. Williams thought that they had two choices: Pay the Indians a whole lot more money or give the land back. To be sure there were difference in theology between Williams and the Puritan fathers. Williams would follow an open admissions policy in Rhode Island. People of various beliefs were welcome in Rhode Island: there was no religious test. It would seem though that Williams' case as in the case of another Puritan expelled from Massachusetts Bay, Thomas Morton, the dispute over land rights was the defining issue.