In a brief statement, Interjet said the workers had been grounded while "a series of evaluations are finalized." It said security is its top priority and it rejects "any manifestation of violence."
According to screenshots of social media posts, Ximena García, said to be a first officer for the airline, wrote: "A bomb should fall on the Zocalo" — Mexico City's sprawling downtown plaza — "... it would do us all a favor (hashtag)vivaMexico."
"P.S. if you are bothered by my comments, erase me, believe me that I don't give 2 pesos cordial regards," the post continued.
Another woman who has been identified as an Interjet worker responded: "I support you," adding a crying-with-laughter emoji.
This weekend the square filled with tens of thousands of people, many of them backers of President Andrés Manuel López Obrador, to hear him give the "Cry of Dolores," the traditional reenactment of priest Miguel Hidalgo's 1810 call to arms that launched the war for independence.
López Obrador is highly popular in opinion polls but also has long been a polarizing figure, with many who dislike him feeling and expressing intense disdain for him and his supporters.
The comments took off online, with lots of users directing critical tweets at Interjet and the two women.
A number of politicians and other prominent public figures also weighed in. López Obrador called the remarks "very strong and irrational." Some called it a bad joke. At least one senator demanded firings.
In a video that circulated online Wednesday, García apologized to her company, the president, the country and "the people I offended."
"I deeply regret the comment I made on my social networks. It was an immature comment, not thought out," she said. "The people close to me, my family, my friends, know that I am completely against violence. I would never incite violence. I want to truly apologize."