It's more like: "Because we have arrived at a model that describes well most other aspect of those particles and their behavior, and has verified predictive power, and given the constrains and calculations based on that model, that's what its charge would be".
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.
" We show that the symmetries of this non-commutative space unify the standard model of particle physics with (2) chiral gravity. The algebra of the octonionic space yields spinor states which can be identified with three generations of quarks and leptons. The geometry of the space implies quantisation of electric charge, and leads to a theoretical derivation of the mysterious mass ratios of quarks and the charged leptons. Quantum gravity is quantisation not only of the gravitational field, but also of the point structure of space-time."
i.e. it's the only combination that works. A proton is a bunch of other particles that, when combined together, balance out an electron. The 'why' is 'because that's a stable configuration' in the same way that water at 25c is liquid not gas because the 'rules' of the local environment dictate that.
I mean, why do those particles exist at all? That's really what you're asking. Why do electrons exist, why do protons 'form' from subatomic particles to balance them out? Existential kinda question.
