Newton made a dramatic break with the orthodox mechanical philosophy of his day, the philosophy that was generally understood by the most advanced thinkers at the time to be the most promising method of approaching the study of the natural world. He did not reject the entire system of mechanical thought, but he did reject one of its most basic assumptions: that force could be transfered only by the impact of one material body with another.
I would not want to us to be obliged to appeal to miracles in the ordinary course of nature, and to admit absolutely inexplicable powers and operations there. Otherwise, on the strength of what God can do, we would grant too much license to bad philosophers, allowing them those centripetal virtues or those immediate attractions at a distance, without it being possible to make them intelligible... This is, in fact, a return to occult qualities or, what is more, to inexplicable qualities.