This election cycle marks only the third time that the nonpartisan publication endorsed anyone - first Lincoln, then Lyndon B. Johnson.
“As a publication whose founders declared it to be ‘of no party or clique,’ we don’t make political endorsements lightly,” Atlantic editor Scott Stossel wrote in a statement about the decision to endorse Clinton. “We have historically only endorsed a president when we felt that the stakes had been elevated to a true national emergency, or an existential threat to the republic. We believe that the election of Donald Trump poses such a threat, which is why we’ve decided to endorse Hillary Clinton.”
The endorsement of a historically significant president such as Lincoln seems more obvious, but the endorsement of Johnson perhaps less so.
As background information, Johnson faced off against a Republican senator named Barry Goldwater. Much like their endorsement of Hillary Clinton, The Atlantic did not seek to promote Johnson so much as they hoped to protect the nation from Goldwater.
According to their article on Hillary Clinton, "Goldwater’s limited capacity for prudence and reasonableness was what particularly worried The Atlantic."
They view Trump in a similar light, in addition to his being the most under-qualified candidate in over 200 years of our nation's history:
"Donald Trump, on the other hand, has no record of public service and no qualifications for public office. His affect is that of an infomercial huckster; he traffics in conspiracy theories and racist invective; he is appallingly sexist; he is erratic, secretive, and xenophobic; he expresses admiration for authoritarian rulers, and evinces authoritarian tendencies himself. He is easily goaded, a poor quality for someone seeking control of America’s nuclear arsenal. He is an enemy of fact-based discourse; he is ignorant of, and indifferent to, the Constitution; he appears not to read."
You can read their endorsement, Don't Vote for Trump, here.
Perhaps most noteworthy about the article is that the mix of both conservative and liberal editors, as with the situation against Goldwater, do not intend to promote Hillary Clinton's specific policies or agenda.
As they describe the threat that Trump poses, they explain that this is a safety measure against the irreparable harm he would do to the Constitution and to the world. They admit Clinton's flaws as "exasperating," and represent both Republicans and Democrats in their voting history.
Yet they have united, for just the third time in 200 years, in an effort to protect our nation against "a demagogue, a xenophobe, a sexist, a know-nothing, and a liar." They continue, "He is spectacularly unfit for office, and voters—the statesmen and thinkers of the ballot box—should act in defense of American democracy and elect his opponent."