I think that modern physics has definitely decided in favor of Plato. In fact, the smallest units of matter are not physical objects in the ordinary sense; they are forms, ideas which can be expressed unambiguously only in mathematical language.
-- physicist Werner Heisenberg
Science is curious about both what is larger than humans can see (stars, galaxies) and what is smaller (bacteria, atoms). Humanity has long sought the smallest of the small -- is there anything so small that it cannot be divided?
In classical physics, everything in the external world is divided into matter ("stuff" like rocks, water and flesh) and energy (like fire, lightning, and heat). This division sits very well with the naive realist: I can slap my hand against a brick wall and feel that it is solid. It is 'stuff.' Scientists discovered that all stuff -- solid, liquid, or gas -- is made of combinations of materials called, elementarily enough, elements. Elements include familiar substances like gold, iron, and oxygen. All 'stuff' that isn't a pure element is a compound of elements; for example, water is a compound of hydrogen and oxygen.
The naive realist may be a little confused as to how two elements can make a compound that appears nothing like either of the two elements, but at least the concept of elements mixing together to make stuff makes sense.
With the birth of modern physics, it was found that elements aren't so elementary after all. In fact, it was determined, elements are actually made of smaller pieces called "atoms." The word "atom" was chosen because it is the Greek word for "unable to be divided," and the newly discovered atoms were obviously the smallest stuff possible.
In the new scientific view, each element had its own particular type of atom, and these atoms could join together to form molecules. This joining together creates the illusion of "elements" and "compounds," which are simply mental tools for us limited human beings to understand how free-floating atoms interact with each other.
With atoms, scientists figured out things that were mysteries before. Before atoms, no one really knew where heat came from; after, it was figured out that atoms move, and this motion releases energy -- voilà heat. The faster the atoms move, the more energy they release, the hotter the substance. (Of course, as the sophisticated realist is quick to point out, 'substance' is just a shorthand way of saying 'group of atoms large enough to be seen by humans.')
Atoms were still "stuff," but they introduced a new view of stuff. Far from being solidly fixed in space, just sitting there, atoms were feisty little critters, always energetically moving about. This is of serious concern to the naive realist, whose solid wall is no longer just standing there, but teeming, pulsating, moving. It certainly doesn't seem to be moving, and naive realists are certain that what seems to be, is.
Another cherished assumption atoms do away with is the idea of things separate from each other. When the scientist looks at the atomic level, there is no boundary, no absolute dividing line separating one thing from another. When my hand touches the wall, there is a point at which one cannot say whether a particular atom belongs to the wall, or to my hand. When my hand is not touching the wall, there is a point at which one cannot say whether a particular atom belongs to my hand, or the air around it. Atoms are continually joining and leaving. Our sense of smell, for example, is actually the detection of molecules floating through the air from what we are smelling. When we say that we smell a rose, if we mean (as the naive realist does) that we are actually smelling the rose, we are wrong; atoms from the rose are constantly streaming out into the air, and some of them land inside our nose. It is those atoms, which can no longer be said to be part of the rose, that we smell.
And so our poor naive realist is permanently left out of science at this point. Sophisticated realists may continue; they understand that our perception of the wall is a limited view, and that the motion simply occurs at a size and rate that is undetectable by unaided human senses. The illusion of solidity and stability is just that, an illusion created by the limits of our senses. Further, we do not see the wall, touch the wall, or smell the wall; our seeing, touching, and smelling is an interaction between atoms and energy. The light waves we see are in our eyes, not the thing seen; the molecules we smell are in our nose, not the thing smelled. Our sight tells us something about a thing which is not seen, and our smell tells us something about a thing which is not smelled; but they are not those things.
As so often happens, the name "atom" ("indivisible") turned out to be a bit arrogant. Modern science quickly found out that atoms weren't the smallest things after all. Atoms are made up of even tinier bits of stuff, named electrons, protons, and neutrons, which were obviously the smallest stuff possible.
What's more, not only are the atoms moving, but inside the atom, electrons are spinning wildly around the center ("nucleus") of protons and neutrons. In fact, atoms do not really exist as separate things, but are just mental shorthand for "a group of electrons spinning around a nucleus." It turns out that all elements, all atoms, are made up of the same protons, neutrons, and electrons; the number of protons determines all the varied properties of atoms and elements. What makes iron different from gold is simply a different number of protons, neutrons and electrons.
Don't wake up the naive realist, because there is something really unusual here. If we zoom in on the surface of our solid, motionless wall, we see that it is made up of moving molecules, held together by energy (electromagnetic force). The forces holding the wall molecules together are strong, as are the forces holding together the molecules in my hand; this is why, when I slap my hand against the wall, it doesn't go through. Not because the "stuff" in the wall is taking up too much space; it turns out that there is more empty space between molecules than there are molecules.
If we zoom in further, we see that each molecule is made up of atoms, which are also moving around violently. And there is more empty space than atoms in the molecule!
Zooming in still further, we find that the each atom is made up of electrons spinning crazily around a nucleus. For comparison, if the nucleus were the size of a orange, the electron would be a pinprick over four miles (10km) away, with nothing but empty space in between!
By this time, the idea of "stuff" -- especially solid, motionless stuff -- is completely dead. Anything you look at has more empty space in it than stuff. I'm not even talking about space that has only air in it: air, too, is stuff that is mostly empty space. I'm talking space that has no stuff in it.
As science progressed, it discovered that electrons, protons and neutrons aren't the smallest stuff after all. There are even smaller things, with funny names like "quark" and "lepton." As you might guess, they move around a lot.
Studying these little critters, along with Einstein's theories of relativity, has led many to rethink to their opinion of what reality is.
For Further Exploration
The technically minded and curious can browse these sources elsewhere on the Web: