Blaming Islam for the September 11th attacks strikes me as both intellectually incorrect and tactically unintelligent. As such, interfering in the construction of an Islamic cultural centre near the former World Trade Center site in Lower Manhattan seems unjustified and inappropriate. That being said, it does seem that there are general characteristics of religion that played a role in the attacks: specifically, belief in a god with an interest in human affairs and belief in an afterlife. Both quite plausibly motivate people to do things to their fellow human beings that they would not, if they were convinced that ethics are entirely a matter of human thought and behaviour and that this one life on Earth is all we get to experience. People who believe that there is no god out there to please or offend – and who believe that death is the end for them – would probably be a lot less likely to kill their fellow human beings on the basis of religious motivations, and more hesitant to risk dying themselves in the process (though people have committed suicide attacks for non-religious reasons).
Of course, it would be politically impossible in the United States for a public figure hoping to get re-elected to say that religion in general could be a problem, and that it would be equally inappropriate (or appropriate) to build a mosque, synagogue, or other place of worship in this part of New York. As such, the minimum that can be done in the interests of equal treatment is not to block the building of the cultural centre, and in so doing blame an entire faith for the actions of a few fanatics, while at the same time targeting problematic beliefs within one faith that are also present in others which have not been singled out for criticism.
There are certainly forms of religion that do not generally incite or justify violence, but they tend to involve a fair bit of doubt: doubt that a single set of rules must be followed by everyone, doubt that a particular religious authority is always right, and a refusal to unconditionally accept religious teachings when they clash with reasoning or evidence.