I have been reading Knight's book on teaching physics and I now think that the issue may be far simpler: Most people don't believe in Newton's Laws. Students frequently worry about forces applied during the launching of the projectile and what happens to the projectile after it hits the ground. (Always confused about "initial" conditions and "final" conditions.) I think they are uncomfortable with the fact that the means by which the projectile is launched is irrelevant - how it is brought to a stop is irrelevant -gravity is irrelevant to the horizontal motion - fast things are accelerating just as much as slow things, etc...
Laws are memorized, equations are manipulated, and answers are obtained - but most people do not change the way they think things work.
I saw some students at other times of the day and made some terrible analogies based on what they were doing at the time:
1) A student working on his music composition theory homework: "Think of the bass cleff as the horizontal motion and the treble cleff as the vertical motion: same rules but slightly different roles." (nervous laughter followed by eye rolling)

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