Mathematically it works out that way because the standard model is build up from symmetry groups. The hand wavy explanation is that the symmetries observed in nature wouldn't be reproduced if the charges differed by random irrational numbers.

The same is also generally true of other conserved quantities in the SM. Noether's theorem unifies symmetries and conservation laws as the same thing.

As far as a more fundamental explanation as to WHY the universe is this way, ask your god i guess.