Newton’s work, particularly the laws of motion [wiki] and universal gravitation [wiki], had been used by some people to argue against the existence of God. Newton himself, however, said:
"Gravity explains the motions of the planets, but it cannot explain who set the planets in motion. God governs all things and knows all that is or can be done."
"This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent Being. … This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called ‘Lord God’ [pantokrator], or ‘Universal Ruler’. … The Supreme God is a Being eternal, infinite, absolutely perfect."
"Opposition to godliness is atheism in profession and idolatry in practice. Atheism is so senseless and odious to mankind that it never had many professors."
(Source: Isaac Newton’s Religious Views [wiki])