Why Does Religious Conviction Endure Exposure?

The questions you are asking could be approached at several levels, only some of which I can hope to offer. But it seems to me that you want most to understand what it felt like to hold these ideas so "experience near" that they aren't objects of study, but fundamental emotional commitments conditioning all cognitive experience, the way atheism conditions yours, or mine. John Winthrop is such a valuable literary companion because he conveys in his writing precisely this experience, as---to give one example---Roger Williams, for all his force and brilliance, cannot. I would suggest Ed Morgan's brilliant brief evocation of Winthrop in this context, in The Puritan Dilemma. From there, the next stop would be Perry Miller's New England Mind: The Seventeenth Century, which is far less terse, as befits a much more comprehensive view of the subject.