What stood out from that comment [1] was the following:
In this book the term had distinctly negative connotations as Young questioned both the legitimacy of the selection process used to become a member of this elite and the outcomes of being ruled by such a narrowly defined group.
You could argue that successful startups (as well as other successful companies in any category) do something similar with their selection processes (aside from the fact they they do not have or exercise political power). Colloquially, the term "meritocracy" has come to imply "organization with clear and rigorous standards that hires, promotes, and fires based on such standards".
Maybe it's not a perfect word, but there seems to be some general consensus about what it means and what people are aiming at. Perhaps it's better for an organization to be more humble and to strive to be a meritocracy, even if it knows it can't do it perfectly.
If you don't have some concept of "merit" - based on job-specific skill, communication with others, emotional regulation, self-discipline, general effectiveness - how can you staff a company at all?
[1] I assumed you meant https://news.ycombinator.com/item?id=7406566
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edit:
(based on clarified response in child post - thanks @steveklabnik )
I don't really see much distinction between the intention of "we try to hire good people" and "we objectively determine who the best people are", aside from the humility in the first statement and the hubris in the second one. If there were a process to objectively determine 'merit' for some company and job, people would be all over it. And 'merit' is obviously conditioned on the particular tasks to be done, the culture of the workplace, and a pile of other factors.
Bottom line - to be overly hubristic is not good. But striving to define your company's concept of merit is not a bad thing - it can only help in making better decisions in hiring and promotion.