They're relevant for site owners, sure, but flash ads aren't a very good argument for, "without flash, users won't get the full web user experience". Presumably nobody will refrain from buying an iPad because of flash ads not working on it.
Hm. Without rich-media advertisements, maybe web content producers would not make as much money from their sites and have less motivation (and capital!) to create great content?
If there were no such thing as Flash, then the web would be different. Whether it would be better or worse is open to personal interpretation, but I don't think that your selected quote is the most egregious thing in the article.
It just sounded to me like he was trying to make it sound like most of the top sites were using Flash for their own content, when it's more likely they are only displaying someone else's ad.
I don't have a problem with ads, though Google is a good case of not needing Flash to make effective ads.