Rick Hertzberg has been pointing out for years that the founding fathers supporting proportional representation, and only agreed to create a Senate because such a concession was required to win support from smaller states. Following up on his excerpt of Hamilton, he has more:

Hamilton and Madison (Washington, too, by the way; I’m not sure about Jay) strongly favored what was then called “proportional representation.“ (Modern P.R., under which legislative seats are distributed roughly in line with aggregate party shares of the vote, hadn’t been invented yet.) Obama-like, they forced themselves to pay what they knew was a corrupt and immoral price in order to get a barely acceptable deal—which deal they sold, Obama-like, as a fine, public-spirited solution.
When it came time to decide who would write the essay defending the two-senators-per-state provision, Madison drew the short straw. In The Federalist No. 62, little Jemmy did not bother to conceal his lack of enthusiasm for the task:
The equality of representation in the Senate is another point, which, being evidently the result of compromise between the opposite pretensions of the large and the small States, does not call for much discussion.
Just a little discussion, in which Madison frankly admitted that the deal was a political bargain that had nothing do with high-flown republican principles or democratic theory. It would be pointless, he wrote,
to try, by the standard of theory, a part of the Constitution which is allowed on all hands to be the result, not of theory, but “of a spirit of amity, and that mutual deference and concession which the peculiarity of our political situation rendered indispensable.” A common government, with powers equal to its objects, is called for by the voice, and still more loudly by the political situation, of America. A government founded on principles more consonant to the wishes of the larger States, is not likely to be obtained from the smaller States. The only option, then, for the former, lies between the proposed government and a government still more objectionable. Under this alternative, the advice of prudence must be to embrace the lesser evil; and, instead of indulging a fruitless anticipation of the possible mischiefs which may ensue, to contemplate rather the advantageous consequences which may qualify the sacrifice.
In other words, the small states made a non-negotiable demand. Madison, Hamilton, and the other grownups realized that the only alternative to giving in was the failure of the Convention and a reversion to the Articles of Confederation, which would be even worse than a government with a screwed-up Senate. So they caved, and now they’re doing their best to stop worrying about the Senate and focus on the good aspects of the proposed new governmental setup, which will probably be less bad (“the lesser evil”) than the status quo.