Newtonian mechanics was resisted throughout its history, all the way until it was replaced by relativity and quantum mechanics. But the criticism did not so much concern the specifics of his laws of motion, there were few Aristotelians around, and, after all, they were pretty well confirmed by experiments, as their interpretations and "metaphysical" implications.
When Newton published Principia the prevailing view inof physics was Cartesian, and the two of them clashed over the course of 19th century. Cartesian physics, was more qualitative, descriptive and "intuitive", in other words, it was more like the natural philosophy of old (e.g. Aristotelian or atomistic). Descartes had the luminiferous aether, and the swirling vortices in it moving things around, in place of Newton's faceless mathematical forces, including the action at a distance for gravity, which even Newton himself disliked. In the early 1700-s Cartesian physics was refurbished by Malebranche and Rohault into an alternative to Newton's. Here is from Iltis's The Decline of Cartesianism in Mechanics:
Newton's absolute space also got its share of detractors. First, Leibniz, who saw space as relational rather than a self-standing metaphysical entity, Berkeley shared similar views and thenoffered an influential criticism of Newton's mechanics, albeit less known now than his criticism of Newton's calculus. Then Kant, who sought to produce a physical construction for the "absolute frame of reference" in almost modern spirit. He associates it with the ideal limit of taking first the frame attached to the Earth, then to the center of mass of the Solar system, etc., see Newton and Kant on Absolute Space by Friedman. These ideas were later be used by Mach to dispense with the absolute space even in the mathematical formalism, and usher in the relativistic conception, adopted and transformed by Einstein.