I've been flying commercially over Iran on the way to my final destination mostly uniterrupted for more than a decade, two or three; nor do I see why it would have been on the "list" mentioned in the OP. (Same could be said for North Korea too, but I just don't end up on flights where that would be happening.) Can't say the same for Iraq and Afghanistan, but I've been flying commercially over Afghanistan on the way to my final destination for at least the past four years.