Skeuomorphic icons are probably OK, but skeumorphic behavior is horrific. Consider the awfulness of the Mountain Lion era address book and calendar that tried to emulate the behavior of physical objects by imitating their limitations. That, for me, was the nadir of OS X usability. It might have been great for someone who'd literally never seen a computer before, but anyone who wanted to navigate a calendar without flipping through months one page at a time had a real fight on their hands.
If you want an icon that looks like a physical object, OK. I can probably live with that. But the moment you want to extend that to making the app act like the object its icon represents, you've lost me. Perhaps Ive et al decided that having a realistic Notes icon attached to a non-notebook-like app was more confusing than keeping the old one? That certainly seems justifiable.
Also: who cares what the Safari compass looks like? To me, "compass" means "compass". It's never represented a safari to me (not that "safari-the-adventure" represented "Safari-the-browser"). What would that skeumorphic icon be anyway - a rifle?
This is what we used to have: http://venturebeat.com/2012/10/30/skeuomorphic-design-or-one... . I couldn't have been happier when Mavericks ditched all that. It wasn't perfect, to be sure, but it went a long way to restoring artificially-lost usability.
The article feels to me as though the author is caught up in nostalgia. That's fine, but not mistake "I liked it that way" for "that way was objectively better".