There is a difference, I think, between a building that is being currently used and a building that is not being currently used. If one had to chose which to replace, which one would be replaced first? I think the former.
The Trade Centers were a focus of activity in New York, and were seen by many as a symbol of economic prosperity. This is one of the reasons that they were targeted by Al Qaeda. The replacement of them is a form of communication to the world that New York will not be frightened by terrorists.