I think actually you're a bit confused about the difference between instrumental virtues, like courage, and inherent virtues, like benevolence. (Which list "rationality" goes on is actually a tricky one for me. In a certain sense, Stalin seems terrifyingly rational.)

I guess we could talk about "intellectual courage" versus "physical courage" or something like that, and your argument is that these men were not intellectually courageous. But usually when people say "courage" simpliciter, they mean a willingness to act in spite of a high risk of pain and death. And this the hijackers definitely had!

Indeed, there's something truly terrifying about the Al Qaeda hijackers: They were mostly right about their moral values. They were altruistic, courageous, devoted to duty. It's only this very small deviation---"maximize deference to Islam" instead of "maximize human happiness"---that made them do such terrible things.

This also meshes with what we know about the Milgram and Zimbardo experiments; quite ordinary people, if convinced that they are acting toward a higher moral purpose, will often do horrific things. The average Nazi was not a psychopath, not a madman; he believed that what he was doing was right. And this should be the most chilling fact of all.