No. If what worked before continues to work, it means it's not broken.
Also: What "very basic functionality" doesn't the latest versions of Safari support?
IE6 continues to work fine for what it supported originally as well.
To my knowledge, file downloads worked in all browsers prior to mobile Safari being initially released. So Apple did release a browser that broke some quite basic web functionality.
Regarding Apple's insistence on not supporting Ogg (Vorbis|Theora) (I assume that's what you're alluding to), those codecs were briefly recommended by the HTML5 standard, but were later dropped.[1] Again, I think its a stretch to say that Apple broke anything, simply because they resisted a proposed standard. I know a lot of developers were disappointed, but that's how committees work: You don't always get it your way.
[1] https://en.wikipedia.org/wiki/Use_of_Ogg_formats_in_HTML5
I think one unfortunate aspect of the article is that it focuses on some of the less common deficiencies of Safari. I would have called out mobile Safari being unable to download files, or Apple's insistence against video codecs that all other vendors are aligned in agreement on when it comes to video.