Roughly speaking, it is because the strong nuclear force which binds quarks together is stronger than the electromagnetic force which would otherwise spread the charge more equally. But also, quarks have charges of $e/3$ or $2e/3$ so you can't get a charge of $e/2$. So then the question becomes why do quarks have these charges, and why is charge quantised in the first place? That is a long story, but a fascinating one. I don't think one can give a brief answer, except to say that it is to do with the way complex numbers behave, and it is to do with symmetry, and the way quantum physics works.
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