Why doesn't matter pass through other matter if atoms are 99.999% empty space?

The ghostly passage of one body through another is obviously out of the question if the continuum assumption were valid, but we know that at the micro, nano, pico levels (and beyond) this is not even remotely the case. My understanding is that the volume of the average atom actually occupied by matter is a vanishingly small fraction of the atom's volume as a whole. If this is the case, why can't matter simply pass through other matter? Are the atom's electrons so nearly omnipresent that they can simultaneously prevent collisions/intersections from all possible directions?