Well, both points of view have a point.
The central idea of Unix is that everything is a file. Files are just streams of bytes on disk. Most happen to be text. Text is just streams of lines. And then you write a bunch of simple tools that handle files, bytes, and lines, and they will combine really well for more complex tasks.
However this was (and in many corners still is) a radical idea. The natural tendency in virtually every other system, from the Macintosh to IBM mainframes, was to store data in various structured records. Whether we're talking resource forks or records, you always, always, always add structure of various kinds. The idea of just scanning through bytes to find, say, the end of a record is shockingly inefficient.
So we have the point of the article. HFS+ breaks Unix. If you don't see that, then you don't actually understand Unix. The filesystem ignores one of the founding central concepts, with the result that the entire Unix toolkit and way of thinking about the world doesn't work. Standard utilities, scripts, etc don't know that resource forks exist, and will do the wrong thing with them. If you walk into OS X and are told, "It's Unix under the hood", well that is a lie. It really isn't. You can work within it and only do Unix things and it will work, but as soon as you access things from elsewhere in the Apple ecosystem, things break in ways that they wouldn't in, say, Linux.
But we also have your point of view. There are very good reasons that HFS+ works the way it does. And it is integrated into the UI in ways that date back decades. And THIS is true. OS X was an attempt to put a Macintosh UI on a fork of Unix. And preserving central concepts of Unix really were not as important as making the UI work right. With the same features. With data being reasonably easy to port between the two systems, and programs not unnecessarily different.
Both points of view are valid. Which one matters depends on what you're trying to do. Furthermore it is natural, not stupid, that a person who has just had a major plank pulled out from under their way of understanding the world tends to have a strong emotional response.
"OMG, you broke everything! The tools that I rely on don't work and I have no idea what else is broken!" This is an extremely common response. This is one of the reasons why it can be hard for programmers to switch languages and environments.
As it happens, I personally understand both points of view. I have over 20 years of experience with both Macs and Unix. This is typed on an Apple laptop. But fundamentally I agree with the article. Apple broke Unix. I recognize that there is no solution at this point, and I mostly confine myself to living within the Unixy parts of the system. But HFS+ got it wrong and is not well integrated with the command line. I mean look at this. If you have myfile you can look at myfile. Then ls myfile/..namedfork and get an error. Then ls $file/..namedfork/rsrc and see more stuff??? And I can only know to do this if I know it is there to be seen???
That's just broken.