Earlier quoted context omitted.
You should ask yourself the opposite question: why should the large states tolerate lack of proportional representation indefinitely, given that it's not in their best interests? And the thing is, if large states find that the present arrangement stymies their interests too much (which is increasingly the case due to polarization on the federal level), and there's no legal way out of that bind, they can set legalitie…
I agree that equal representation isn't in the best interests of the more populous states. The problem is that there's a fundamental tension here. Regardless of differences in population size, it's not reasonable for the legal system in a less populous state (say Idaho) to be dominated by the interests of those in a more populous one (say California). Neither is the reverse acceptable (for Idaho's interests to domina…
That it was appropriated to justify the massive expansion of federal power is another matter, but, well... given how absurd Wickard was, I'm pretty sure that if it weren't the Commerce Clause, it would have been something else.
As for majority voting, all alternatives are strictly worse. The problem, rather, is that there's no meaningful democracy at federal or even state level, because there's no meaningful representation at that scale - the "representatives" are anything but. I'm not sure there's such a thing at any scale, actually - for all the purported benefits of representative democracy wrt preventing mob rule, history has plenty of counter-examples, including US here and now (it's a minority mob rule, which is even worse).
I'd rather have direct democracy, but only so long as it's truly deliberative (i.e. not just people voting on a list of yes/no questions put in front of them, like referendums - think more along the lines of, say, how the Constitutional Convention worked). And scaling that requires some form of council democracy, with enough levels that meaningful deliberation remains possible on every one of them, all the way to the top.