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If Newton's theory was simply taught because its how the universe was percieved in the past, then courses would simply mention it in passing. Instead they devote whole chapters, tests, and exersizes to it. It would be like teaching every astronomy student the old geocentric model of the solar system in several chapters and tests.
Newton's theory is taught because it is a simplified version of the truth that suffices except for untypical cases. Teaching students the simple version first helps them ease into physics, before relativity and quantum mechanics are thrown at them. Newton's theory isn't wrong, it just isn't the full story. The same goes for the theory of evolution. There will always be room to improve and details we haven't figured out yet.
Perhaps you're right abut why it's taught, but I still cannot agree when you say "Newton's theory isn't wrong" because it is fundamentally wrong in the way it defines space, time and action-at-a-distance; yes numerically we get results that are more than adequate for most practical applications but I'm not referring to numerical accuracy when I describe it as wrong.
If you do still think it isn't wrong and it just isn't the "full story" then it follows that the "old geocentric model" isn't wrong just not the full story too.
Acceleration is not relative to an aether, light trajectories are not unaffected by gravitation, clocks do not all tick at the same regular rate irrespective of motion, of gravitation - this is where Newton was wrong.