He's been clear that there's no ideological component to terrorism, and that the 9/11 terrorists were actually thugs. I'm sure he's sympathetic with the mischaracterization of Islam.
He spoke at the Arab American Institute in Dearborn on the heels of what I presume were unauthorized anti-Israel ads paid for by supporters which he forgot to correct, so why wouldn't Dr. Paul be comfortable with an endorsement from a Muslim paper?
He'd simply say that he has no control over who supports him or their ideologies. He certainly wouldn't return their donations.