The OP is spot on. I've seen the military and the civilian world now, and I think those who are criticizing might be missing the point.
The piece is not trying to say that FOs should "take charge" more, rather that they are poorly trained in the civilian flying industry to be the real "Captain Support Officer" that they really could, and should, be.
"My four stripes beats your three..." is a big part of the problem, along with non-existent leadership (not management, there is a difference) training in the civilian aviation sector. FOs going out of their way to help is, more often than not, met with suspicion and disdain from a lot of Captains, who were themselves never taught how to really be that support guy. Especially true outside the highly structured 121 world. Consequently, many--instead of properly utilizing a good FO when they're fortunate enough to team up with one--are threatened, and so proceed to beat all intitiative out of said individual.
Unfortunately, those FOs eventually become Captains, and the cycle perpetuates itself. In a world where one must go along to get along (as well as keep one's job), where one butthurt Captain or CP senior to you means cleaning out your locker with no good explanation, future cockpit leaders are poisoned and rarely recover.
There are exceptions--when my trips started out on day one, leg one with the Captain saying "We're in this together--I consider you a co-captain, I'm just the guy who signs the paperwork..." it always put me at ease and made me want to help the guy out as much as possible. Even though I still knew that at the end of the day HE'S still the Captain (and I never forgot it), with all the attached rights and responsibilities. Because he gets it. Unfortunately, I see the opposite far more often in the time I've spent at multiple companies now in the civilian world.
Yes, there's no rank in the cockpit in the military world. Or in the debrief either, for that matter. But then I never had to worry about being able to make my mortgage or feed my family or have a bad reference follow me around for a lifetime because I spoke up. That's ALWAYS in the back of my mind now, and it leaves a bad taste in my mouth.
So, I'll continue to be a good Lieutenant, Captain Support Officer, FO, whatever you wanna call it, whenever that's my role, and set the example at every opportunity. And when I'm the Captain, I still consider it part of my duty to grow the FO in the other seat into a good Captain Support Officer too--which, by the way, is usually in every company's Captain job description... Not just make sure he's got a hotel room and knows the bus time in the morning. 'Cause he'll upgrade one day too, and if he doesn't learn how from me, then who?!