The quarks that make up a proton (or neutron, etc) have charges that are multiples of 1/3 the electron charge. So in one sense that is the real unit charge. But because as far as we know quarks can never exist in isolation we can only ever see particles with multiples of the electronic charge.

The number assigned to charge is an arbitrary convention. You could assign quarks with full numbered charges, instead of fractions, but you'd have to rework and recalculate all of physics and chemistry to get the new values right, and that's just too much work.

No matter what arbitrary value you assign to the electric charge, quarks will always be 1/3 of that. That's the problem in question, not the absolute value.

So quarks have a charge of 2 or -1, and a two of the former and one of the latter make a proton, which therefore has charge 3. An electron is elementary, but also has charge 3. The question is: that seems like a weird coincidence, how come it's like that?