It really shoudn't, and the reason is geopolitical.
Which nation was most supportive of the dynamics that facilitated 9-11? Saudi Arabia. The U.S. is not going to invade Saudi Arabia, but it would like to influence the liberalization of Saudi society.
When the Bush administration wanted to remake the region, it had to look at all of the destabilizing elements of the region. What were the other nations, other than Iraq, that were procatively destabilizing the region through their support of Jihadist elements? Yes, Iran was (and is) one. So is Syria. Syria is a huge problem because Israel is the scapegoat for everyone's problems in the region, and Syria does more than their fair share to keep the Israeli-Palestinian conflict going.
No, lets go to the map...
Guess which nation borders Saudi Arabia, Iran and Syria? Iraq.
What was the only nation in the Middle East that was genocidal at the time of 9-11? Iraq.
The moral imperitive was there to invade Iraq, and this coincided with a clear strategy to remake the Middle East. No nation needed change more than Iraq, and they, unlike Iran, were unable to change from within due to the brutally oppressive nature of the regime.