Isaac Newton was known as a highly devout man during his lifetime, doubts about his religious orthodoxy began to circulate immediately after his death. Chiefly responsible for these rumors was William Whiston, Newton’s successor as Lucasian Professor of Mathematics at Cambridge University and a champion of his scientific work. Soon after Newton’s death, Whiston published a short account of his private religious convictions in A Collection of Authentick Records (1728), proclaiming that Newton had held what most of his contemporaries thought of as scandalous and even heretical views about the doctrine of the Trinity. According to Whiston, Newton believed that the doctrine was a terrible fabrication devised in the fourth century and that Athanasius, the great Alexandrian bishop, was “the grand and the very wicked Instrument of that Change” and the architect of the corruption of original Christianity.
For years, Whiston had publicly hinted at Newton’s heresy, hoping thereby to support his own anti-Trinitarian positions, which, unlike Newton, he widely professed. For those views Whiston had been expelled from both his college fellowship and his professorship at Cambridge. His claims about Newton went largely unheeded, partly because most refused to believe something so hideous about Britain’s greatest natural philosopher (the contemporary term for a scientist), and partly because Whiston, having rejected the authority of tradition himself, was thought to be an untrustworthy source. However, Whiston had in fact accurately captured Newton’s radically unorthodox views. For almost all his adult life Newton harbored a guilty secret that he revealed only to a trusted few, and he skillfully put off those who probed too deeply. Publishing these ideas would have made him widely reviled and would have earned him, like it did Whiston, expulsion from his university. Had this happened early in his career, Newton would never have composed his great scientific works, and his seminal mathematical contributions (including the discovery of the differential and integral calculus) might never have been recorded for posterity.
Newton’s strenuous efforts to prevent his private views from becoming more broadly known had the long-term consequence that his religious writings remained largely hidden for over two centuries. Indeed, they are only now being published in full as a result of the online Newton Project...
Church, Heresy, and Pure Religion - The New Atlantis