Actually, he denied the divinity of Christ, insofar as he felt that Christ was subordinate to God the Father, and considered Trinitarianism to be a false doctrine. In fact, he wrote a book about exactly that, entitled "A Historical Account of Two Notable Corruptions of Scripture," but realized it would be too dangerous to publish it in England under his own name. He tried to get John Locke to have it translated and published in France, but Locke wasn't able to make the necessary arrangements, and so it was never published. But it makes a nice Isaac Newton fairy tale to say that he was a strict Christian and Biblical literalist, doesn't it?
It appears that Newtons fear was of corruptions of scripture that were tied to trying to reinforce the trinitarian position, not that Jesus wasn't God.
The quotes from his book that I have read (I have not read the book) seemed to say he didn't think the trinity was clearly spelled out in the scriptures and that scholars may have added text to reinforce or clarify the doctrine of the trinity, therefore if it wasn't clear, sans the corrupted text, he could not spell it out as a doctrine.
I wish I could get my hands on a copy of the book to know first hand Newtons positions in the context of his analysis.