btw, is it currently illegal or something to have a plot about actual Islamic terrorists? Did they have to make it American traitors?
It is something of a cliched, discredited, and rather racist trope to stereotype Arabs and/or Muslims as terrorists. It certainly would not be a good thing to embrace that trope uncritically. There's also the fact that this is a mystery show, remember, so it's supposed to engage in misdirection. We're conditioned by fear and ignorance to expect terrorists to be Middle Eastern and/or Muslim (and to mistakenly assume those are automatically the same thing), and so a mystery story wishing to mislead us about the identity of a terrorist would naturally lead us to suspect a Middle Eastern or Muslim character and then reveal otherwise.
Besides, it's just true to life. In the hours after the Oklahoma City bombing, the media pundits were all jumping to the conclusion that it was an Islamist attack until it turned out to be the work of domestic anti-government militants avenging Ruby Ridge and Waco. And that was six years before 9/11 (although two years after the first al-Qaeda bombing at the WTC). The "Arab terrorist" stereotype has been around in American mythology for quite a while, so it would be a smart move for any aspiring terrorists to find Arab or Muslim patsies to blame for it. As Fallon's reactions showed, it's just the sort of thing we'd fall for.