Why the strong gut reaction to a mosque at Ground Zero, to be commissioned on 9/11? Maybe due to the historic practice of co-opting conquered enemies' religious places and re-establishing them in the religion of the conquerors. It sends the not-so-subtle message that the conquerors' deities are more powerful than those of the conquered, taking psychological warfare to the realm of the afterlife. We can argue 'til the cows come home about whether an international financial center constitutes a religious place per se, but that is exactly how hardcore Islamists would characterize Western religion/culture.
To be sure, this was (to my knowledge) primarily a Catholic practice, both in the Middle East and in South/Central America. That is, I don't personally know of any churches which were later transformed into a mosque by a conquering Moorish force - but that could just be there weren't many churches overtaken in the wake of the Crusades.
In any case, middle age Cordoba in Spain *was* a place where all three religions peacefully coexisted for a time --under a Muslim ruler.