If we look at the counter arguments, muslims were among those killed in the attack, and as even GW Bush said, they were not targetting Islam, but terrorism.
Now if 911 had been the result of a concerted attack by the religious organisation of Islam, then it would be more clear cut.
For example, if the Pope and his Cardinals planned to carry out terrorist attacks on Tel Aviv in retaliation for the Jewish assassination of Christ, then I can understand that building a Catholic Church on the ruins would be kind of insane, not to mention bad taste.
I guess the rationale is that relatives of the Muslim businessment killed in the WTC would want somewhere to reflect their loss. The Americans are pretty big on religion, so I'd be guessing that they'd also want to built a hand clappers assembly hall there, along with a Synogogue perhaps, and that it would somehow be bigger than the proposed Mosque.
What they should really do is have a multi-faith building for all the Abrahamic faiths and just make sure they put hoses in the toilets and serve Kosher and Halal foods. (Same concept as a coffee machine that serves different types of espresso)
After all, it's basically one religion, albeit one that rears its ugly head whenever there is tragedy in this world.
The question arises, why would they want to bother? The facility would just be desecrated and make life even worse for the surviving relatives of any persuasion.
Keep the religious places away from there. Whatever you do, the Lutherans will continue to say that the Synod Lutherans are all going to hell, that the Muslims are all terrorists and that the Jews.... well we don't criticise the big-noses, do we?

Good post Amadd. Just what I'd expect from a moderate Indonesian like yourself