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

Things are not empty space. Our classical intuition fails at the quantum level.

Matter does not pass through other matter mainly due to the Pauli exclusion principle and due to the electromagnetic repulsion of the electrons. The closer you bring two atoms, i.e. the more the areas of non-zero expectation for their electrons overlap, the stronger will the repulsion due to the Pauli principle be, since it can never happen that two electrons possess exactly the same spin and the same probability to be found in an extent of space.

The idea that atoms are mostly "empty space" is, from a quantum viewpoint, nonsense. The volume of an atom is filled by the wavefunctions of its electrons, or, from a QFT viewpoint, there is a localized excitation of the electron field in that region of space, which are both very different from the "empty" vacuum state.

The concept of empty space is actually quite tricky, since our intuition "Space is empty when there is no particle in it" differs from the formal "Empty space is the unexcited vacuum state of the theory" quite a lot. The space around the atom is definitely not in the vacuum state, it is filled with electron states. But if you go and look, chances are, you will find at least some "empty" space in the sense of "no particles during measurement". Yet you are not justified in saying that there is "mostly empty space" around the atom, since the electrons are not that sharply localized unless some interaction (like measurements) takes place that actually forces them to. When not interacting, their states are "smeared out" over the atom in something sometimes called the electron cloud, where the cloud or orbital represents the probability of finding a particle in any given spot.

This weirdness is one of the reasons why quantum mechanics is so fundamentally different from classical mechanics – suddenly, a lot of the world becomes wholly different from what we are used to at our macroscopic level, and especially our intuitions about "empty space" and such fail us completely at microscopic levels.

Since it has been asked in the comments, I should probably say a few more words about the role of the exclusion principle:

First, as has been said, without the exclusion principle, the whole idea of chemistry collapses: All electrons fall to the lowest 1s orbital and stay there, there are no "outer" electrons, and the world as we know it would not work.

Second, consider the situation of two equally charged classical particles: If you only invest enough energy/work, you can bring them arbitrarily close. The Pauli exclusion principle prohibits this for the atoms – you might be able to push them a little bit into each other, but at some point, when the states of the electrons become too similar, it just won't go any further. When you hit that point, you have degenerate matter, a state of matter which is extremely difficult to compress, and where the exclusion principle is the sole reason for its incompressibility. This is not due to Coulomb repulsion, it is that that we also need to invest the energy to catapult the electrons into higher energy levels since the number of electrons in a volume of space increases under compression, while the number of available energy levels does not. (If you read the article, you will find that the electrons at some point will indeed prefer to combine with the protons and form neutrons, which then exhibit the same kind of behaviour. Then, again, you have something almost incompressible, until the pressure is high enough to break the neutrons down into quarks (that is merely theoretical). No one knows what happens when you increase the pressure on these quarks indefinitely, but we probably cannot know that anyway, since a black hole will form sooner or later)

Third, the kind of force you need to create such degenerate matter is extraordinarily high. Even metallic hydrogen, the probably simplest kind of such matter, has not been reliably produced in experiments. However, as Mark A has pointed out in the comments (and as is very briefly mentioned in the Wikipedia article, too), a very good model for the free electrons in a metal is that of a degenerate gas, so one could take metal as a room-temperature example of the importance of the Pauli principle.

So, in conclusion, one might say that at the levels of our everyday experience, it would probably enough to know about the Coulomb repulsion of the electrons (if you don't look at metals too closely). But without quantum mechanics, you would still wonder why these electrons do not simply go closer to their nuclei, i.e. reduce their orbital radius/drop to a lower energy state, and thus reduce the effective radius of the atom. Therefore, Coulomb repulsion already falls short at this scale to explain why matter seems "solid" at all – only the exclusion principle can explain why the electrons behave the way they do.

If it were possible for one object to pass through another object, then it would be possible for one part of an object to pass through a different part of the same object. Therefore the question asked here is equivalent to the question of why matter is stable. See this question on mathoverflow. That question was more about the stability of individual atoms, but in my answer there, I gave a reference to a paper by Lieb. Section II discusses the stability of bulk matter. The argument depends on both the properties of the electromagnetic interaction and on the Pauli exclusion principle. Therefore anyone who tells you that the stability of bulk matter is purely due to one or the other of these factors is wrong.

The same holds for the normal force. People will try to argue that it's only due to electromagnetic interactions or only due to the exclusion principle. That's wrong for the same reasons.

Although Lieb's treatment is complicated, there is a pretty straightforward argument that quantum mechanics is necessary for the stability of matter. There is a theorem called Earnshaw's theorem that says that a classical system of interacting charged particles can't have a stable, static equilibrium. It's not a difficult or deep result; it's just an application of Gauss's law. Letting the equilibrium be dynamical rather than static doesn't help, since then the charges would radiate.

In answer to the main question, matter does, in fact, "pass" through other matter. Starting from the macro scale (stars , galaxies), down to the micro scale (atoms), it happens all the time. The "free" movement of matter starts to get impeded, as the atoms start making latices (solids, crystals). But even at this scale, as Rutherford demonstrated, matter (alpha particles), passes matter (thin film of gold). It's only at the scale where one is trying to "pass" atoms at a distance equal or less that the outer electron orbit (orbital), that you run into electrons repulsive forces and the Pauli exclusion principle, which do prevent matter "passing" matter.