And yet he clashed with the church on matters of dogma...
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"What disturbed him most was the concept of the three-in-one nature of God. Newton found the Holy Trinity not only illogical, but abhorrent. He had read the works of an early Christian named Arius. This writer denied the divinity of Jesus, and Newton fully embraced the idea. He could not, therefore, swear to believe in the Holy Trinity when, in fact, he did not."
Yes, he was a believer, in his own way, and none of it had any bearing on the scientific body of work he created, be in the principia mathematica or the contribution to newtonian physics. He saw it as the description of the mechanisms through which, in his belief, god built the universe.
You will find 1000's of other significant scientific figures having all kinds of religious beliefs or lack of such beliefs. Having the same importance to their scientific contribution as their opinion on prefering cats or dog, being vegan or meat eater, pineapple on a pizza or who's the best Beatle