I think it’s an overstatement to claim that matter is made of atoms. That claim is literally false. Most matter is not made of atoms, if you take the normal definition of atom which is something like “a nucleus and a bunch of electrons in a stable configuration acting as a single entity”.
Most obviously, stars are mostly not made of atoms–they’re mostly made up of plasma, where there’s a giant soup of nuclei and electrons that aren’t particularly attached to each other, which I don’t think count as atoms. There are real atoms in the atmosphere of a star, but that’s only a tiny proportion of its mass. White dwarves don’t have atomic structure either—the electrons aren’t localized around nuclei. Neutron stars are made out of neutrons, so there’s definitely no atoms there. The sparse matter which is between stars or between galaxies, which is the majority of the mass in the universe (!) (not including dark matter), is also not mostly made of atoms. It’s apparently a plasma-like mix of protons and electrons.
(We don’t know whether dark matter forms atoms. I would bet it doesn’t, though, because dark matter seems to interact only through gravity and possibly the weak nuclear force, neither of which looks like it permits atom-like things.[1])
So what is made of atoms? Planets, molecular clouds, interstellar dust, and other stuff like that. But most of the universe isn’t like Earth and I think it’s misleading to act as if it is.
In the excellent introduction to his lectures on physics, Feynman wrote:
If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generations of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all things are made of atoms—little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another. In that one sentence, you will see, there is an enormous amount of information about the world, if just a little imagination and thinking are applied.
I think that it’s interesting to note how untrue this is on a cosmic scale. If you zoom out as far as you can and look at how the universe behaves, the first thing you’ll notice is the gravitational behavior of matter. Gravity doesn’t behave like things are made out of little particles, it behaves like mass is continuously distributed. The next thing you might see in the universe is the stars, which behave according to plasma physics and are heated by nuclear physics, neither of which behave in a way very similar to Feynman’s description[2]. White dwarves and neutron stars can be described quite nicely without ever describing their constituents as particles.
If I was teleported into this universe from another, I would not have guessed that in some tiny pockets, it supports the kinds of complex, stable interactions that lead to chemistry and to life. I’m glad that my initial guess would have turned out to be wrong!
[1] I don’t think either of these forces support stable configurations of matter, where by “stable” I mean that they bounce back to their original state when you push them a little. For the weak force, this is because it doesn’t support bound states, and for gravity I don’t have a proof, but I suspect it to be true. As Adam Scherlis points out, dark matter could interact with itself by other forces and maybe form atoms via those forces; I think I would overall bet against this based on a simplicity prior but I agree it seems possible.
[2] Nuclei are clumps of particles that are repelled from each other by the electromagnetic force at long distances, then attracted by the strong nuclear force at short distances (which makes fusion possible), and then are repelled again once the particles get very close to each other (otherwise nuclei would have zero radius). This is different to the interactions between atoms, which don’t have the long distance repulsion.