First, as an historical matter, the writer is absolutely correct: The Constitution never would have been written and then ratified in 1787 had the Connecticut Compromise not given the small states disproportionate power in the Senate. But the same can be said about compromises with slaveowners. These were both necessary given the political circumstances of the moment. Delaware was prepared to walk out, with some other small states--Rhode Island never even bothered to show up in Philadelphia--and torpedo th eConvention. Madison in fact was despondent about the Connecticut Compromise and even gave brief thought to leaving the Convention, but he (correctly) decided that achieving even a flawed Constitution was better than no Constitution and the high probability of a "United States" that would very shortly divided itself into three countries along the Atlantic seaboard.
So the question is why we, 220 years later, should feel so in thrall to a compromise reached on raw political grounds. We certainly wouldn't feel any similar commitment to the compromises on slavery, nor, to take a modern example, should those of us who support the United Nations feel committed to maintain support for a veto system in the Security Council that can be explained only by reference to the particular "great powers" that won World War II.
I'm not so antagonistic to small states as I might sound. BUT, I see no good reason for giving them extraordinarily disproportionate power in the 21st century, power that they use, as any political scientists, including Madison, would predict to line the pockets of their constituents while being relatively disregardful of the needs of the overwhelming number of Americans who live in larger states and big cities. If we were talking about "ordinary" affirmative action (which, I should say, I tend to support, although with some reluctance), we would be talking about quite marginal benefits, e.g., the use of race or ethnicity as a "tie breaker." No one would suggest, though, giving his/her "favorite" ethnic or racial group 50 times the voting power of majority whites.
There is a long and commendable tradition in the US of concern about "tyranny of the majority," and the Senate is often defended as a barrier against that. But we should recognize that one can also have de facto "tyranny of the minority," which is another way of referring to an indefensible status quo that is basically entrenched because the Constitution makes it next to impossible to engage in fundamental reform.