No, Morocco is very much Muslim. Damn near 100%. But they're a tiny portion of overall Muslims and the name Moussaoui, while popular there and elsewhere of Moorish descent, is not a widely popular name elsewhere in the Muslim world.
The point is that, even looking at the passenger manifest just picking out "muslim-sounding" names, the name Zacarias Moussaoui probably would not have thrown any flags because it sounds more Israeli than anything. And that still doesn't address Richard, Dan, Brian, and Oliver; the names of some others that have been arrested.