Their fans gave them a pass on those comments, but this time is different. The main reason they're catching so much grief is that they've built a fan base of patriotic Americans feigning love of country and respect for the military with songs like Travelin' Soldier.
Country Music, as a sort of mainstream subculture, has always projected patriotism. Long before 9/11, fans jammed into concerts by the likes of country superstars Brooks and Dunn--waving flags and singing along with songs like Only In America...
The Chicks exercised their right to free speech, but in doing so, if nothing else, they violated a simple rule of business: Do not insult your customers. (In politics: Don't alienate your base.)
I should add, the article's author implies a double-standard that Fred Durst's comments were met with cheers. But remember, he was playing to his base, not alienating it.