Turns out the reason was slavery. A huge proportion of the Southern population was enslaved, and slaves didn't vote. The free staters didn't want slaves to even count toward state population for the purposes of congressional apportionment, while the slave staters did, so they compromised on counting the slave population at 3/5 of the free population. As a result, prior to the abolition of slavery, the votes of free men in slave states were always represented at a higher proportion than the votes of free men in free states.
Many of the founders were wise and educated men who thought carefully and critically about how to establish a sustainable republic. But to do so, they had to win the votes of a cross-section of the American establishment of the time, many of whom thought that owning human beings, using them as farm labor, and whipping them if they disobeyed were morally acceptable things to do. And upon making a series of political compromises with these people, they had to rationalize those compromises in such a way to make them palatable to the general public.
This is, of course, no longer relevant.
But it is still relevant for just about all the reasons it was relevant then.
Another major factor is that Americans mostly see themselves as citizens of the USA first, and citizens of their state a distant second.
This is of course by design. The founder's obviously knew about proportional representation and they deliberately chose to disregard it. Shouldn't that give you pause to figure out why?