Pearl Harbor was (and is) a military target. So is the Pentagon. However, there are different types of targets out there. For example, there are tactical targets like weapons depots and military units where you're directly trying to weaken the enemy on the battlefield. On the other hand, there are strategic targets like factories, petroleum infrastructure, economic infrastructure, and the like where you're trying to undermine the enemy's entire government.

In that regard, the World Trade Center was a strategic target. OBL and company intended to deal a harsh blow to our economic system (and arguably succeeded) which is the source of our strength as a nation. To them, the WTC was a legitimate strategic target and their actions acts of the war they declared on us in 1998. It was also a highly symbolic target because it represented most of what they hate about the West.

Yes, Japan is a nation and her armed forces attacked us in 1941. That is the real difference between the two attacks. It's a lot harder to target terrorist networks than nations. Still, both were acts of war and must be dealt with harshly. Failure to do so will only encourage the next group that wants to attack us.