Thank you for your reply!
The power of Captains is not absolute in SF, and they are required to follow certain procedures and rules. There is a chain of command, just as in any military command structure, but I would hardly call it godlike. Army cadets are required to follow their captains in the US military as well.
The only difference is that the workers of Star Fleet (which is different from the Federation) do not have the threat of wages hanging over them. If they get sacked from their position, after a review from Star Fleet, they get unlimited healthcare/housing/food/etc. The power dynamic is completely different from businessmen who control peoples very livelihoods.
Now Star Trek takes place in a more technologically advanced future so compared to us they are like Gods, but they same logic would apply to us today if we traveled back in time to the medieval era. That's a completely separate issue from what's brought up in this article.