Just two comments. Mainstream Arab Muslims have completely and utterly denounced the attack just as much as anyone else. You just hear on the news the one or two groups/idiots who didn't.
Also, the problem is with some members of two groups -- Arab Americans and those of the Islamic faith. There are over 7 million Arab Americans and probably 20+ million more who look Arab American in the US. That is not a small group. And those of Islamic faith? Many, many more.
And there's no way to tell a citizen from a non-citizen by the way. Domestic air travel does not require a passport.