Twin Towers were a symbol of peace and prosperity. Pentagon, hardly a symbol of peace, has been rebuilt. Twin towers weren't. The message that this sends to the public is hardly positive.
The fact that the Twin Towers weren't rebuilt is a symbol of defeat of the american way of life. Actually, the currently planned status of the WTC site is one giant advertisement for the success of terrorism.
The facade of Twin Towers would be an excellent place for various peaceful artwork. The whole facade could be partitioned to squares, which could hold either a decent collection of static pictures or - better yet - large digital screens, like those on the Times square. The best place for those advertisements would quite naturally be the places of impact of the aircrafts. Furthermore, the observation deck(s) on the rebuilt towers would imaginably become rather attractive location for various public gatherings.
Memorial for the victims. The best memorial for the victims of 9/11 and the ensuing wars would definitely be rebuilt Twin Towers, not two uglish pits.
The Bible speaks of rebirth. The Twins should be reconstructed (somehow), since the new testament speaks of rebirth.
Practical aspects. Twins just were integral part of the city. It's just too impractical not to rebuilt them (in some form), too costly. Or 9/11 itself was not enough (for us) - we have to cut ourselves even more. Even though we have computers and communicate through them, there are other means of communication. When the Twins were destroyed, New York was struck at its core, certain behavioral schemes were abolished. A city, a civilization is like a living organism. One cannot live with(out) fundamental organ(s) taken out.
There are many historical examples of reconstruction. After WW2, whole cities were rebuilt.
Old memories, old symbols. What's gone, is gone. The Towers looked like a giant number 11. Built in the end of sixties and beginning of seventies, with some finishing touches added shortly thereafter, they were not exactly new. They felt down because they could not withstand the heat of fire, which spread rather quickly inside them. They were attacked on the 11th of September. 2001.
Twins were one and only. Rebuilt ones would be no substitute for the original. You just cannot rebuild things.
The Bible (one of ten commandments) says don't substitute god with symbols. The omnipresent presentation of the Twins as symbols of America goes directly against this commandment, as would the reconstruction.
The price of reconstruction would be like pool in a sea. The rebuilding of the WTC would cost only a fraction of the expenditures already spent on the War on terrorism, not to mention the cost of wasteful bailouts.