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The question also touches on an important concept in modern science, which, when understood, can help you answer many other deep questions.
This is the concept of "collective behavior," the idea that large collections of things (such as molecules in air, cars in heavy traffic, people in a long line at a coffee shop) often behave in simple and beautiful ways which are quite different than the behavior of the individuals.
Sound, including the sonic boom, is an example of such collective behavior, where an incredibly complex collection of trillions of trillions of tiny molecules all moving in their own different directions with their own different speeds and bouncing from one another create the familiar and relatively simple behaviors that we all hear in our daily lives.
So, to answer the question, very much like a single car cannot make a traffic jam and a single customer at a coffee shop does not break into a spontaneous conversation with himself, a single molecule, even when moving faster than the speed of sound, cannot create a sonic boom.
The class's thinking was along the right lines, but it's not that the booms are too small to hear, it's that you need many, many molecules to make a sonic boom, not just one.
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