He was wrong about certain features of the universe such as universal time and was not aware of relativistic effects but this does not upend his domain.
What if Newton were not wrong? What if he was correct in stating that both time and space were absolute? Look for example at the case where someone goes to meet someone on a Wednesday at a café in New York. A week later he returns to the same Café at the same time, again on a Wednesday, to meet the same person. As far as he is concerned nothing has changed he has returned to the same place on the same day of the week, at the same time to meet the same person. We are aware that during that time interval; the earth has been rotating on its axis at a speed of 1600 km/h approx. apart from that the earth has also been speeding around the sun at a speed of something like 107,000 km/h and at the same time the sun has been tracing a path through the Milky Way Galaxy at 514,000 km/h and the Milky Way Galaxy leaves them all in the shade by moving around the Universe at 2,000,000 Km/h. So nothing is the same, nothing is as it was. The first question is how can that be? What strange force causes events on earth to remain synchronized in spite of the huge distances and times that have taken place in the interim? The second thought that occurs is, is that it doesn’t really matter what has moved, or how far or how fast it has moved; because the aether remains stationary and unchanging. This means that all positions can be plotted with reference to the aether, which acts like a Universal frame of reference. “Great Supposition you say!” But, I ask you to consider the question of Dark Matter, according to recent research, and before the crazy theory of Dark Energy came along, it was calculated using sophisticated instrumentation that Dark Matter constitutes 90% of all matter in the Universe. Here is a quote from the Department of Energy USA: “Dark matter makes up about 85 percent of the total matter in the universe, accounting for more than five times as much as all ordinary matter. Dark matter played an important role in the formation of galaxies and the evolution of the universe.” Although here the estimate is given at 85% and not 90%.
That aside, consider the properties of Dark Matter, it has such low interaction with matter, that it is estimated that it can travel through a block of lead a light year thick without experiencing any interaction whatsoever and vice-versa. At the same time Dark Matter exerts a pervasive gravitational force. But the truly incredible property of Dark Matter is that it offers zero interaction with any type of electromagnetic radiation; everything from Radio-waves to Gamma rays can travel without the slightest interference from one side of the Universe to the other. Amazing. Just as amazing is the fact that these are identical (not taking into consideration the farcical luminiferous aether concept) to the properties the so scorned aether was once thought to possess. The Ancients might have been smarter than we thought. If you would like to read more about this theory, consider reading "Redefining the Electron" available on Amazon.