There may be no reason that humans can know as to why it’s mostly empty space. It’s a little like asking why the surface of the earth is 70% water – that’s just the way it is.
I wonder if you’re asking *how* an atom can act or feel solid when it is mostly empty space. The answer to this (as I understand) is the electro-magnetic force. Atoms don’t have to be solid throughout in order to rest on each other or be non-permeable. Instead, they connect and repel through their electrons. When two non-bonded atoms are pushed next to each other, the repulsion of their electrons keeps them apart, creating the physical rules that we see as solid matter.
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