Not spending 2 hours in traffic every day alone is such a huge improvement to my life. Add the ability to live in cheaper areas and being able to make a quick run to the store. Plus I see my family way more!
In particular, the NYT authors don't consider that "jobs that can be remote" tend to have different demographics (more highly educated, more female, more dem-leaning) than jobs that cannot be remote. All of these traits correlate with use of counseling, anti-depressants, etc.
So it's entirely possible that the rise in unhappiness among "remotable" workers is an artifact of who is more likely to have those jobs, and the underlying tendencies of those populations.