The Dixie Chicks were referencing their 2003 controversy
Controversy erupted over the Dixie Chicks in 2003 following a critical comment vocalist Natalie Maines made about American President George W. Bush while performing in a concert in London, United Kingdom. In relation to the forthcoming invasion of Iraq, Maines said, "...we don't want this war, this violence, and we're ashamed that the President of the United States is from Texas."
Taking the Long Way was the first studio album released by the Dixie Chicks following the controversy, the band's reaction to which forms the major theme of some of the songs in the album. Most notable among these is "Not Ready to Make Nice", which was written by all three band members (Maines, Emily Robison and Martie Maguire) along with Dan Wilson, as an expression of band's reaction to the banning of their songs from country music radio stations, and their thoughts on freedom of speech.
The band went on to the October 25 episode of The Oprah Winfrey Show to promote the documentary film Shut Up and Sing and the music video of the song was quickly shown. While interviewing the band, Winfrey said the song is so well written that someone cannot even tell if it concerns the controversy. Indeed, Maines said that she and the other songwriters wanted the song to have a universal interpretation. However, the final lines of the fourth verse are unequivocally about the death threats the band received during the 2003 Top of the World Tour: "And how in the world Can the words that I said Send somebody so over the edge That they'd write me a letter Saying that I better shut up and sing Or my life will be over."
Some other lines in the beginning of this same verse are about a scene featured in the documentary Shut Up and Sing, in which a mother, who was protesting the Dixie Chicks at one of their concerts, is goading her young child to say "screw 'em!":
"It's a sad sad story When a mother will teach her Daughter that she ought'a hate a perfect stranger."
In the song, "daughter" was used instead of "son" as a matter of poetic license.