Alikhan is strongly anti-Israel; he has referred to the terrorist organization Hezbollah as a “liberation movement.” Hezbollah is on the U.S. official terrorist list while being an affiliate of the Muslim Public Affairs Council. Alikhan also opposed President George W. Bush’s prosecution of the war on Islamic terror. In 2007, Alikhan was instrumental in removing the Muslim terror tracking plan in Los Angeles. The Muslim '‘Mapping’' Plan of the Los Angeles Police Department is now “dead on arrival” according to Chief William Bratton. “It is over and not just put on the side,” said Chief Bratton in a meeting with the Muslim leadership of Southern California at that time. The meeting was moderated by Arif Alikhan.
During his years in Los Angeles, Alikhan was responsible for derailing the Police Department’s plan to monitor activities within the Los Angeles Muslim community, where numerous radical mosques and madrassas existed, and where some of the 9/11 hijackers had received support from local residents.
It's not that he is Muslim, it is that he has a history of undermining national security. And this is no broad brush, they are specifically discussing the actions of the individual(s) in question. Do you really want someone like that in a position of power in the DHS?
We should oppose people for what they have done. That he is muslim isn’t surprising given what he has done, but it is the deeds that disqualify him, not his religion. In My Opinion.