We understand matter perfectly well. Look at the size and scope of the engineering marvels that have been constructed on the surface of this planet and in our low orbit. It's astonishing.
What we don't understand is the fundamental structure of that matter or of our Universe. I personally feel that the people ostensibly "in charge" of this effort are a little chagrined at their decades of inability to produce not only a cohesive result but even a reasonable intermediate explanation that they intentionally couch these problems in the most arcane and impenetrable language available to them.
In any case, you shouldn't feel discontent for humanity, as we've simply discovered all the easy problems, cleverly worked out all the average problems, and now all we're left with is the intractably hard ones. It's very likely that a different type of effort we haven't engaged in yet will be necessary to make progress.
I think there's a useful distinction to be made between "we understand it" and "we can make use of it." Certainly the latter is true, as you describe in your examples. I don't know that it implies the former, though.
I mean heck, even something as mundane as concrete is still the subject of active research as to the chemical reactions and complexities involved.
I guess it's more a spectrum of understanding than a yes/no situation.
For myself, I find it exciting to keep discovering how little we understand, despite our abilities. We seem to be barely a step removed from alchemy, from some points of view.
I think the distinction is more "we understand it" and "we can explain it." Understanding doesn't generally imply totality of comprehension.
Going the other way, you most likely cannot explain why your body or your brain works, yet, here we are, using and understanding them just fine.
Which leads to what I was trying to get at. Perhaps our tentative understandings and our means of receiving them are what gets in the way of deeper comprehension.
I personally don't think perfection is actually achievable, so I'm completely unwilling to accept your definition of our present state as "failing miserably." That's a rather miserable point of view and I prefer to have and encourage hope.
What we don't understand is the fundamental structure of that matter or of our Universe. I personally feel that the people ostensibly "in charge" of this effort are a little chagrined at their decades of inability to produce not only a cohesive result but even a reasonable intermediate explanation that they intentionally couch these problems in the most arcane and impenetrable language available to them.
In any case, you shouldn't feel discontent for humanity, as we've simply discovered all the easy problems, cleverly worked out all the average problems, and now all we're left with is the intractably hard ones. It's very likely that a different type of effort we haven't engaged in yet will be necessary to make progress.