Contrary to many other people, I really don't see anything derogatory in the article, and no indication that it's trying to "de-hero" the passengers.
In fact, it goes out of its way to quote a lot of folks who specifically say that they're still heroes even in the new scenario, and doesn't even try to find anyone to disagree.
It's just saying, prior popular belief had the passengers actually grappling with the hijackers in the cockpit, but the actual events were somewhat different.
I think the line that people are reading negatively is, "This theory...discounts the popular perception of insurgent passengers grappling with terrorists to seize the plane's controls." But I think it's a mistake to read that as "discounts the perception of heroism". Instead, it's just literally saying, it contradicts the notion that the passengers were literally fighting over the controls of the plane at the time it went down.
For people who wonder why the article was written and presume an ulterior motive, the fact remains that this is newly released information, and disseminating information is the news media's job.