To briefly summarize the case against Rauf, the most important points are that he seems to praise much of the ideology of Iran’s repressive theocratic regime, refuses to admit that Hamas is a terrorist group (which should be a no-brainer even if you think that Israel’s policies in Gaza are unjustified), claims that the US was “an accessory” to the 9/11 attacks, and sometimes draws a kind of moral equivalency between US foreign policy and Al Qaeda. Weiss also points out that Rauf took part in a bogus “peace organization” organized by a prominent Malaysian anti-Semite.Glad to hear he denounced the 9/11 attacks. It is useful to distinguish moderates like him to the extremists and terrorists. But let's not confuse his views with those of Christian Americans.
As Young notes, there are also more positive attributes to Rauf’s record. For example, he has denounced the 9/11 attacks, criticized some radical Islamist groups, praised the US Constitution, and urged Muslims to respect women’s rights.
Update: Just today, Hamas has claimed credit for the terrorist murder of four Israeli civilians, in order to protest the pending peace talks. Meanwhile, Reuters reports that Ground Zero Muslim center may get public financing. So your tax money could be supporting a group that supports terrorists.
Also, Rauf refuses to criticize the recent Hamas attack, saying "The issue of terrorism is a very complex question".