From your link:
Federal officials said Monday that Padilla, 31 -- who also goes by the name Abdullah Al Muhajir ...
Why does the press keep referring to him this way? Whenever a government spokesperson talks about him, they use his Muslim name, only occasionally mentionining his original name. Do sports writers talk about, "Cassius Clay -- who also goes by the name Muhammed Ali ... Lou Alcindor -- who also goes by the name Kareem Abdul Jabaar ..."

Do they have a problem with the fact that he apparently didn't file official name-change paperwork in the U.S.? Or is this their not-so-subtle way of thumbing their collective nose at the government's not-so-subtle attempt to make him appear more alien (and thus frightening) by only using his Muslim name?

Although I believe the government's decision to use his Muslim name has little to do with a respect for his wishes, and everything to do with making him sound more foreign, I still think the media should use his Muslim name.