I definitely don't think it's wrong. That song is not "bashing" America. It is just questioning certain things that are considered acceptable in our country that he does not necessarily agree with. By the end of the song, he realizes that "noone's right and noone's wrong" ... that's what makes it "America."
I will admit, though, that I did (momentarily) think the same thing when I was listening to it ... that it probably wasn't the best time to question the ways of our country ... but I got over it quickly.
After all ...
It's not like the Dixie Chicks are singing backups on it or anything!