Rather than engaging the main thrust of Michael Hirsh's essay claiming that the US has become a bastion of Southern intolerance, I'll instead make a cheap shot about a detail:

What does seem foreign to us today is the dedication to free thought and, even more, free moral choice that so dominated the correspondence between those two great minds [of John Adams and Thomas Jefferson]. When Jefferson, in his letter of May 5, 1817, condemned the "den of the priesthood" and "protestant popedom" represented by Massachusetts' state-supported church, he was speaking for both of them--the North and South poles of the revolution. Yet John McCain, even with the GOP nomination in hand, would never dare repeat his brave but politically foolhardy condemnation of the religious right in 2000 as "agents of intolerance." Why? Because we have become an intolerant nation, and that's what gets you elected.

Without wanting to take anything away either Jefferson or Adams or their intellectual seriousness, I think Hirsh's comparison is inapt. There's a big difference between a statement written in private correspondence between two ex-presidents (Adams was out of office for over sixteen years and Jefferson for over eight years by the time this letter was written) and a statement given by a presidential candidate on the campaign trail. It certainly wasn't very politically risky for Jefferson to attack Massachusetts religious laws after he'd left the highest executive office in the land (and some might see the "den of the priesthood" comment as not particularly tolerant, either).
And what did McCain say about the "religious right" in 2000? It doesn't sound like he condemned the "religious right" as a whole back then:

Neither party should be defined by pandering to the outer reaches of American politics and the agents of intolerance, whether they be Louis Farrakhan or Al Sharpton on the left, or Pat Robertson or Jerry Falwell on the right.

He does call Robertson and Falwell "agents of intolerance," but are they the whole of the "religious right"? Maybe Hirsh thinks they are. Though, to be fair to Hirsh, McCain did reconcile with Falwell and did go to speak at Falwell's Liberty University, so McCain obviously has backtracked from that earlier statement.