The hijackers knew that the passengers were trying to retake the cockpit from them, and might well succeed.
So rather than possibly lose to the passengers and end up dead or in an American prison, thus "failing" in the eyes of Allah, the hijackers decided that going for the "sure thing" and crashing the plane immediately and killing 40 Americans (33 passengers, 7 crew) was good enough to earn them their martyrdom. So that's what they did.
The point of the article is that contrary to earlier assumptions that the passengers might have actually broken into the cockpit and been physically struggling with the hijackers for control of the plane when it went down, they actually had not made it into the cockpit (yet) at the time the plane crashed. It's not saying they *couldn't* get into the cockpit, just that they hadn't by the time the hijackers decided to end it on their own terms.
But again, the passenger uprising *was* the reason for it, and they're still heroes who saved countless lives and a priceless national landmark/symbol at the intended target.
If true, this command could have been given during a fight in the cockpit. (I happen to think this is a stronger possibility than not, but there you go.)
In any event, the exact details of what actually unfolded do not matter in the end (and will never be known for certain, anyway), because there is no question but that some of the passengers fought back and were indeed valiant heroes. We know this from solid evidence. Beyond that, it's all theory and guessing games.
Regards,
LH