Without getting into the difficult-if-not-impossible-to-answer question of whether a PhD is "worth it or not", I would like to point out that the author of the linked article is at the tail end of a process that is both lengthy and difficult (both intellectually as well as emotionally). As such, their perspective on the value (or lack thereof) of their degree is probably not at its most objective, and they also have not yet had the opportunity to see for themselves how well (or how badly) their new skills transfer to life outside of graduate school. From experience, I can say that the six month window on either side of defending one's PhD is not a good time to try and reflect rationally about the experience. Call it burnout, call it recency bias, call it whatever you want, but I found that my perspectives on "what it all meant" and "whether it was all worth it" changed quite a lot as I went through the process of writing, defending, and recovering from my dissertation, and then as I entered the workplace those perspectives changed once again (and continue to evolve).

I can safely say that I feel much more positively about the value of my PhD now than I did when I was finishing it; some part of it is increased emotional distance ("time heals all wounds...", etc.), but I think that a larger part of it is that I've had more time to reflect on the experience and am able to more rationally evaluate what I got from it (and what it cost me, in terms both financial and otherwise).