In our culture, we are supposed to resent and dislike bosses. Bosses get paid too much, are mad with power, seek profits over people, etc. In fiction, we are mainly willing to see bosses as good when they run a noble work group, like a police, military, medicine, music, or sport group. In such rare cases, it is ok to submit to boss domination to achieve the noble cause. Or a boss can be good if he helps subordinates fight a higher bad boss. Otherwise, a good person resents and resists boss domination. For example:
The [TV trope of the] Benevolent Boss is that rarity in the Work [Sit]Com: a superior who is actually superior, a nice guy who listens to employee problems and really cares about the issues of those beneath him. … A character that is The Captain is likely, but not required, to be a Benevolent Boss.
Contrast with Bad Boss and Stupid Boss. Compare Reasonable Authority Figure. In more fantastic works, this character usually comes in the form of Big Good. On the other hand, an Affably Evil character can be a benevolent boss with his mooks, as well.
In The Army, he is often The Captain, Majorly Awesome, Colonel Badass, The Brigadier, or even the Four Star Badass and may be A Father to His Men.
For some lucky workers, this is Truth in Television. For a lot of other people, this is some sort of malicious fantasy. (more)
But here is a 2010 (& 2011) survey of 1000 workers (30% bosses, half blue collar):
Agree or completely agree with:
You respect your boss 91%
You think your boss trusts you 91%
You think your boss respects you 91%
You trust your boss 86%
If your job was on the line, your boss would go to bat for you 78%
You consider your boss a friend 61%
You would not change a thing about your boss 59%
Your boss has more education than you 53%
You think you are smarter than your boss 37%
You aspire to have the bosses job 30%
You work harder than your boss 28%
You feel pressure to conform to your bosses hobbies/interests in order to get ahead 20% (more; more; more)
In reality most people respect and trust their bosses, see them as a friend, and so on. Quite a different picture than the one from fiction.
Foragers had strong norms against domination, and bosses regularly violate such norms. We retain a weak allegiance to forager norms in fiction and when we talk politics. But we also have deeper more ancient mammalian instincts to submit to powers above us. And also, our competitive economy probably tends to make real bosses be functional and useful, and we spend enough time on our jobs to see that.
Many other of our cultural presumptions are probably similar. We give lip service to them in the far modes of fiction and politics, but we quickly reject them in the near mode of concrete decisions that matter to us.
I think the dichotomy you describe comes about because the fiction you are referring to is written by writers and writers are not typical people. They see themselves as artists and are rivalrous with business people. The bad boss is one trope reflecting their worldview.
It's similar to how in the movies, the woman always goes with the creative / artsy / spontaneous guy, not the rich / business-y guy.
"I'd guess even more so in blue collar work: someone with experience with building or whatever would be far better than me at leading on a construction site, even if he had no higher education and had a much lower IQ than me."
You'd still want the most intelligent builder to be the leader of the bunch in the vast majority of cases. Someone obviously less intelligent than you can be an excellent boss, just not for you: if you are working for him that means you also have the skills relevant to the trade, so your boss can't claim his trade specific skills as a reason to be the leader, unless you're socially dysfunctional or your trade is one where experience matters above all, but those aren't common situations I'd wager.