I've been writing a fair amount about the filibuster and majoritarian or antimajoritarian politics in the Senate, and it occurs to me that, unless my memory is wrong, I've never actually talked here about the composition of the Senate. So:
There is absolutely no legitimate democratic justification for the maldistribution of the Senate. Scholars of American politics (and democratic theorists) disagree on lots of things -- the electoral college, simple plurality voting, the filibuster, bicameralism, and on and on, but as far as I know there are no serious scholars who support the composition of the Senate. End of story.
Well, mostly end of story; end of the democratic theory part of the story. The second part of it is that, as far as anyone can tell, it hasn't mattered very much. Some: there are interests that are helped and hurt. The obvious bias is in favor of rural America and against urban America, and if I recall correctly that's what people have found (I've misplaced my proper citation here, but I'm pretty sure that David Mayhew wrote something relatively recently summarizing what's been found, and it isn't much). There isn't, however, any long-term partisan bias. So, we're talking about a problem that cannot be justified, but in the end doesn't seem to matter very much. You'll sometimes see arguments about how groups of Senators representing very few Americans could do something nefarious, but in reality that never happens; Rhode Island and Wyoming tend to split, and so on.
Now, I sort of like the idea of having a different basis of representation in the two Houses of Congress. I also like having one relatively small body (leading to Members who retain as much individual control as possible) and another relatively large body (leading to Members who represent narrower interests, and are willing to trade off their influence on most issues for extra influence over a handful of areas). Those are good Madisonian devices, in my view. But California and Vermont having the same number of Senators? No, there's really no good reason for that.
All of which is, alas, moot; there's no way at all to change it. And, as I said, in practical terms it doesn't matter a lot. But, yes, it's a genuinely Bad Thing.