That's purely by convention. It's just that we fist discovered electrons and protons and quarks with their fractional charges came in much later.

To be clear, we say that an electron has -1e charge: that "e" is the absolute value of the charge of an electron. The charge of an electron is approximately −1.602176634×10^−19 Coulombs. Quarks have either +-2(1.602176634×10^−19)/3 or +-(1.602176634×10^−19)/3 coulombs charge.

It's a fraction because we simply decided it was easier to describe an electron's charge as "e" and quark charges as being a fraction of that. It's entirely by convention.

We could've just as easily have described, like you mentioned, a quark to have either +-q or +-2q charge and electrons have -3q (where q=(1.602176634×10^−19)/3 C). We just happened to find electrons significantly before. It's also convenient as we don't see free quarks so every charge we see in the universe is a multiple of e, there's no advantage to going smaller than that.