I know that Hendrik Hertzberg is a big reformer, especially on things like the U.S. Senate and the Electoral College, but I'm really not sure what the point is of his piece exposing the fact that Virginian James Madison and New Yorker Alexander Hamilton weren't big fans of the Great Compromise that set up the Senate.
Moreoever, whatever they may have thought about representation of political divisions, as opposed to people, the fact that they were reluctant to glorify the virtues of malrepresentation in the Senate in a propaganda piece indented to sway the people of big-state New York is even less telling. Of course New Yorkers (and Virginians) wanted House-style representation of people. It's also a stretch to pick (logical) opponents of the Senate and say that they are the Framers who matter. Presumably, there are other (small state) Framers who were making the argument that of course representation should be equal by state in the Congress, but their states should go along because it was the best they could get.
Now, I happen to agree with Hertzberg (and nearly everyone else) that the two-per-state Senate is a terrible idea, and does not at all comport with generally accepted ideas of democracy. Alas, there's also nothing that can be done about it under the Constitution, and given the relatively small effects it has had, there's no reason to dwell on it. Nor does malapportionment in the Senate really tell us anything about whether the Senate we have should be run as a more majoritarian, more partisan, body.
I do have a question, however: does anyone know whether Madison, Hamilton, or any of the others had anything to say about the principle of one person, one vote within their states (or even one voter, one vote)? I don't really know anything about it, other than that by the 20th century most states were badly malapportioned. Did any of them care about that, back then?