There is no inherent evil in anecdotes. This is obviously fiction and was not intended to be used as evidence. If it were, then you would have a reasonable complaint. The purpose of a little story like this is (from Wikipedia): "to reveal a truth more general than the brief tale itself, or to delineate a character trait or the workings of an institution in such a light that it strikes in a flash of insight to their very essence."

Second, why are the programmers not taking control of management positions if they know so much better?

I see this asked a lot and I don't understand why. First of all, the traits (not skills, but traits) or interests needed for taking control of management positions are different (vastly different depending on the company) than the traits/interests needed to be a good developer. Second, don't forget that our fictional hero Charles eventually quit the company and presumably found a better place. Finding a place that fits you more is sometimes better than trying to change yourself to fit the management mold in a particular company.

I think Alan created the best product for the company.

Did you read the same story I did, or are you rewriting it into your own parable?

Now imagine how good Charles would be if he could learn to cooperate and participate in a group like Alan's.

That would be good I think. Let's also imagine how good Alan could be if he could learn to see past the inflated corporate policies, procedures, and checklists and focus on the crux of the problem.