Well, they're comfortable because the phenomenon is well-studied, we have very good models and can with good accuracy predict what will happen. What we don't know is why exactly it behaves in this way.
The word "why" (and other references to causation) don't work in a normal way when you're talking about fundamental physics, because fundamental physics is the lowest-level model within which causation takes place.
To ask "why" some part of the standard model is the way it is, you either invoke some rubric for comparing models, like Occam's Razor; or you indulge in metaphysics and speculate on the nature of whomever is running the Simulation. Either of these is a different meaning than the "why" of "why do rockets work in space."
Well, you made quiet a few assumptions here. We don't yet know how much fundamental quarks are and what (if anything) hides in the subquark level.
Given the lack of adequate instruments, our minds and unconventional approaches are our most powerful tools at this point. For example, we generally consider the space between particles as void. We can't see anything, we can't detect anything, so we assume there's nothing there. But for what it's worth, there could be trillions of unknown particles that don't interact with matter. So why would it matter, you ask? Because it's not impossible that under certain conditions some of these might cluster into matter or interact with it in unobvious ways. The existence of dark matter and energy (or the related phenomena) indicates this is not impossible.
But yes, I see your point. However, I hope we get deeper into understanding this phenomenon before I die. Who knows, maybe it's because of some yet-undiscovered aspect of photons, and metaphysical speculation is not necessary?
