Materialism does not assert that everything is “matter”. There are the actions, the relationships and the attributes (or properties), NONE of which are physical entities.
Materialism is that everything is reducible to matter and physical forces (energy) and physical laws.
If there is something else in the universe other than material/physical/natural reality, then that needs to be explained and we no longer have materialism.
If you’re saying that we have no explanation for why two parts hydrogen and one part oxygen combine to make something wet and that is water - instead of something that looks like peanut butter. Well, that is unexplained in materialism.
So also are all the physical laws - where did they come from. Why do we have certain chemicals bonding and others not? Why does pressure on graphite create diamonds and not some other thing?
You have not liked the question of origins, saying rather that things just are that way. But that’s not an explanation.
Materialism attempts to explain everything from matter and physical laws, all present in the initial conditions of the universe. But as mentioned, this does not explain the ordering of molecules - the various arrangements. Why isn’t the entire universe just random noise?
We haven’t gotten into fine-tuning but it’s the same question. Why are there certain finely tuned constants in the universe? Physicists struggle with that.
Atheists have come up with their own fairy tale - the multiverse, which can explain anything. It’s a magic, unknown, unknowable, unobservable force that answers all the problems.
Catholics will say that God is a much better explanation for the order we perceive and the fine-tuning and the physical laws. All of these show signs of intelligence involved - because our own human intelligence is the only known source of finely tuned harmonic synergies like what we find, especially in human life on earth.