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Of course, you're right: the physics you are studying make a great many simplifying assumptions (like the biologist who found the ideal food for chickens, as long as the chickens were spherical).
The purpose of studying in this way is not to have you design the next Space Shuttle, but rather to show you how this sort of math works, and to introduce you to principles that will be expanded later to handle real situations, if you decide to go into a scientific or engineering profession. If you can start with F = ma and come up with relationships between mass, force, velocity, position, and time, you're getting valuable practice. And maybe getting a sense of elegance (meaning grace and beauty) in this simplistic mathematics.
Newton himself derived his three laws of motion according to an idealized universe where only the masses and the forces that affected them existed. He did not invent his formulas, but derived them from basic principles; in the process he had to create the set of mathematical tools -- the calculus -- to justify his conclusions. In fact, his formulas work pretty well for calculating the motions of the planets, because you can often consider only mass, velocity, and the gravitational force.
The reference gives a bunch of cross-references to related ideas. You might find it worth while to just take a look at some of them: not necessarily to learn what they mean, but more to see what's out there.
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