There does appear to be a deeper reason, but it's really not well understood.

Consistent quantum field theories involving chiral fermions (such as the Standard Model) are relatively rare: the charges have to satisfy a set of polynomial relationships with the inspiring name "gauge anomaly cancellation conditions". If these conditions aren't satisfied, the mathematical model will fail pretty spectacularly. It won't be unitary, can't couple consistently to gravity, won't allow high and low energy behavior to decouple,..

For the Standard Model, the anomaly cancellation conditions imply that the sum of electric charges within a generation must vanish, which they do:

3 colors of quark * ( up charge 2/3 - down charge 1/3) + electron charge -1 + neutrino charge 0 = 0.

So, there's something quite special about the charge assignments in the Standard Model. They're nowhere near as arbitrary as they could be a priori.

Historically, this has been taken as a hint that the standard model should come from a simpler "grand unified" model. Particle accelerators and cosmology hace turned up at best circumstantial evidence for these so far. To me, it's one of the great mysteries.