Atheism is so senseless & odious to mankind that it never had many professors... Whence is it that the eyes of all sorts of living creatures are transparent to the very bottom & the only transparent members in the body, having on the outside an hard transparent skin, & within transparent juyces with a crystalline Lens in the middle & a pupil before the Lens all of them so truly shaped & fitted for vision, that no Artist can mend them? Did blind chance know that there was light & what was its refraction & fit the eys of all creatures after the most curious manner to make use of it? These & such like considerations always have & ever will prevail with man kind to believe that there is a being who made all things & has all things in his power & who is therfore to be feared. [my emphasis]Of course, Newton was working before the advent of the Theory of Evolution. At the time Newton was writing, there was no plausible natural mechanism that could produce eyes "after the most curious manner" and make use of the refraction of light.
Isaac Newton was something of a theologian, and drafted A Short Schem of the True Religion. He argues against atheism on grounds that would today be called 'Intelligent Design':