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.
I suspect that the Muslim hijackers, in a strange way, thought they were maximizing human happiness by removing Americans from the world.
I have so far distinguished between belief as anticipation-controller, belief in belief, professing and cheering. Of these, we might call anticipation-controlling beliefs "proper beliefs" and the other forms "improper belief". Proper belief can be wrong or irrational, as when someone genuinely anticipates that prayer will cure their sick baby. But the other forms are arguably “not belief at all.”
Yet another form of improper belief is belief as group identification—as a way of belonging. Robin Hanson uses the excellent metaphor of wearing unusual clothing, a group uniform like a priest’s vestments or a Jewish skullcap, and so I will call this “belief as attire.”
In terms of humanly realistic psychology, the Muslims who flew planes into the World Trade Center undoubtedly saw themselves as heroes defending truth, justice, and the Islamic Way from hideous alien monsters a la the movie Independence Day. Only a very inexperienced nerd, the sort of nerd who has no idea how non-nerds see the world, would say this out loud in an Alabama bar. It is not an American thing to say. The American thing to say is that the terrorists “hate our freedom” and that flying a plane into a building is a “cowardly act.” You cannot say the phrases “heroic self-sacrifice” and “suicide bomber” in the same sentence, even for the sake of accurately describing how the Enemy sees the world. The very concept of the courage and altruism of a suicide bomber is Enemy attire—you can tell, because the Enemy talks about it. The cowardice and sociopathy of a suicide bomber is American attire. There are no quote marks you can use to talk about how the Enemy sees the world; it would be like dressing up as a Nazi for Halloween.
Belief-as-attire may help explain how people can be passionate about improper beliefs. Mere belief in belief, or religious professing, would have some trouble creating genuine, deep, powerful emotional effects. Or so I suspect; I confess I’m not an expert here. But my impression is this: People who’ve stopped anticipating-as-if their religion is true, will go to great lengths to convince themselves they are passionate, and this desperation can be mistaken for passion. But it’s not the same fire they had as a child.
On the other hand, it is very easy for a human being to genuinely, passionately, gut-level belong to a group, to cheer for their favorite sports team.1 Identifying with a tribe is a very strong emotional force. People will die for it. And once you get people to identify with a tribe, the beliefs which are the attire of that tribe will be spoken with the full passion of belonging to that tribe.
1 This is the foundation on which rests the swindle of “Republicans vs. Democrats” and analogous false dilemmas in other countries, but that’s a topic for another time.