John McCain said Friday morning he will no longer respond to questions about the article in The New York Times a day before, leaving the newspaper to explain why it chose to publish its lengthy profile suggesting the Arizona senator had a romantic relationship with a female lobbyist and did favors for her clients years ago.

McCain and his aides aggressively denounced The New York Times Thursday, saying the story was false and turning the tables on the newspaper, as conservatives and other prominent editors joined the chorus of criticism. The story, in the works for months, was published at a time when the Arizona senator is poised to lock down the GOP presidential nomination.

Editors at The New York Times began to respond on its Web site Friday to the glut of reader questions and comments, many of which were negative.

After standing by the story Thursday, executive editor Bill Keller wrote on the site that “we all expected the reaction to be intense.”

He said the editors and writers knew some readers would disagree with the decision to publish and that they “wrestled” with their doubts, but that he was “surprised by the volume of the reaction.”

Keller wrote that at the time he issued the online response, there were more than 2,400 reader comments on the site.

He said he was surprised how “lopsided” public opinion was against the paper’s decision, but that few readers seemed to grasp the “larger point of the story.”

Keller said the article, an installment in a broader series of campaign profiles, was meant to point out how the candidate who “prizes his honor above all things” has a history of being careless about his reputation.

That’s where the suggestions about his relationship with lobbyist Vicki Iseman come into play, Keller said.

The original Times article, quoting anonymous sources, described how campaign aides to McCain’s 2000 bid for president wanted to keep him and Iseman apart during that election for fear the two were giving the impression they were having an affair. It also noted how McCain wrote to government regulators on behalf of a client of Iseman’s while he was Commerce Committee chairman.

A Washington Post story Friday also detailed how several members of his 2008 campaign have worked as lobbyists, despite his anti-special interest message.

“Perhaps the defining narrative of Senator McCain’s career is his long, determined recovery from scandal,” Keller wrote.

He added that the paper believed the Iseman relationship was something readers would want to know about their potential president: “Clearly, many of you did not agree.”

One reader wrote, “I must say that the McCain article left me embarrassed for your paper. So little substance, but trumpeted prominently as though you somehow had the goods on him … .”

The reader linked his comments to an article on Slate.com that said, “Regardless of whether he had the affair, McCain wins.”

The New Republic magazine published a long article Thursday afternoon on its Web site detailing the story behind the story and claiming, “What’s most remarkable about the article is that it appeared in the paper at all.”

The New Republic lambasted The New York Times for giving the green light, claiming the piece was “filled with awkward journalistic moves” and that it stepped around the suggested trysts with Iseman by focusing on the debate in the McCain campaign itself about the relationship.

McCain said Friday in Indianapolis that he doesn’t have any more comment on the matter.

“I am moving on. … I addressed every question that was addressed to me. And I do not intend to discuss it further,” he said.

But that isn’t stopping observers, journalists and his own supporters from keeping the story — or the story about the story — alive.

While introducing McCain Friday morning, Indiana Gov. Mitch Daniels made a crack at the Times’ expense.

Urging people to buy McCain’s book, he said: “After you have canceled your New York Times subscription, you will have money leftover.”

Click here to read and submit comments about the McCain story on The New York Times Web site.

FOX News’ Mosheh Oinounou contributed to this report.