[zahllos]

Exactly this. Or to put it another way we don't actually know how the rules of the universe work. So we can't follow a process of deductive reasoning that "why" follows from this or that implication.

Take quantum mechanics. This came out of observations that particles exhibited wave-like behaviour. Mathematics predicts certain things when you start to apply the wave equation. These are then experimentally verified and the model is shown to be pretty good, although it has some deficiencies like not fully linking up with relativity. There are some doubts in some areas of what it predicts as well from what I understand from talking to researchers.

As the article says the original model was that protons were fundamental particles: nothing smaller. This model held up for quite some time but then observational data demonstrated it was insufficient. Same with the three quark model. Knowing the various deficiencies we might go so far as to say "the model that a proton is a +1 charge is good enough" and use that because that works for many situations and that's as much as we need. Although of course, there are always scientists looking to complete the picture.

Science is the incremental acquisition of knowledge through observation and experimentation - and there's an awful lot we haven't figured out.