Unless there's literally seconds until the hijacker will be untouchable, that's likely the most rational choice: play chicken with the other passengers, to see who gets desperate enough to act first.

Now, the moment someone acts, all bets are off - some non-negligible subset may quite likely follow the first person, depending on that persons social standing (people are more likely to jaywalk behind a jaywalker in a suit than one in less formal clothes, for example, if neither of them does anything else to get people to follow - our propensity to deviate from the group behaviour depends on how authoritative the person "leading the charge" appears)

Similarly, if at any point it appears that the hijacker will suddenly become impossible to take out, it becomes more rational to go first, out of the risk that nobody will act.

But the bystander effect is there for a reason: It is generally quite safe to do what everyone else is doing. Except when it isn't.

In terms of hijackings, as it turns out, it is quite safe: Most hijackings, even after 9/11, ends with no dead victims. 9/11 represented a small set of extreme aberrations from hijackings both before and after.

With that in mind, throwing yourself on an armed hijacker only becomes rational once it appears they'll otherwise gain control of the cockpit, at the earliest.