I don't see how a blogger writing two articles about the same subject two years apart means he has "a bone to pick" with the subject, and I don't know why you're assuming that he's writing on the subject because meditation "doesn't work for him". That seems a tad presumptuous. I think it's a plus that the author has actually tried meditation himself, instead of just reading about it. It makes sense that you would try something out if you're going to write about it.

From the first article you linked to:

It’s an interest that dates back to an exchange program (John Denninger, a psychiatrist at Harvard Medical School) attended in China the summer before entering Harvard as an undergraduate student. At Hangzhou University he trained with a tai chi master every morning for three weeks.

“By the end of my time there, I had gotten through my thick teenage skull that there was something very important about the breath and about inhabiting the present moment,” he said. “I’ve carried that with me since then.”

I feel like this is one of the things John Horgan is taking issue with. It's not scientific to have already decided about something before you've done any research. You're supposed to let the research tell you whats going on, not "carry with (you)" some impression you got as a teen.

I don't necessarily think that all the research is bogus or that there is nothing to meditation, but I did think Horgan had some good points. It's also worth noting that even when something does have a benefit, it can still be oversold or misused. Hogan seems to be uneasy about some of the applications of meditation, and some of the culture surrounding it, which I think is understandable.

I didn't notice any interchangable use of the words mindfulness and meditation, but the author does use the term "mindfulness meditation" rather than just mindfulness. The article was admittedly snarky, but not offensively so, IMHO. I don't think it was implied that anyone is dumb or incapable of critical analysis, or that something being popular means it's without merit. Popular things do deserve a bit more scrutiny simply because they affect more people. As for brain scans proving outcomes, the author remains unconvinced for reasons he states in the article thusly:

If people doubt your mind cure, show them brain scans to make it seem more “scientific.” Decades ago, researchers trying to defend psychotherapy against the encroachment of psychopharmacology used this brain-scan tactic. Today, meditation researchers (and advocates) such as Richard Davidson and Sara Lazar are reporting changes in meditators’ brains.

These findings are hardly surprising. All experiences cause neural changes, and the changes are surely more pronounced if you repeat an activity over and over again—whether checking Facebook or chanting “Om.” Meditation may indeed cause changes in your brain, but that finding in itself doesn’t makes meditation’s alleged medical benefits more credible.

The author isn't even against meditation, and plans to try it again. He seems to be wary of overstating benifit without proper evidence, and is unconvinced so far. Meditation is a difficult thing to assess for many reasons. It's totally fine if you find meditation helpful, and I don't think the author meant any offence.

(edit: typos)