Some commercial sites are aspirational, they want their their customers to know they exist out side of some impersonal google search, some places are more your home on the internet that google is, some want to be found through your friends.
I would be surprised if apple, facebook, zynga are in that 90% category and its very hard to say they are "under performing"
Its self important generalisations like that that give SEO as an industry a bad name.
I don't think that's a "pure" statistic. Perhaps StackOverflow users rely on Google returning StackOverflow answers? I know I do; for example, I often append stackoverflow to my programming queries because I know Google will give me StackOverflow answers. Although the referral is Google, I am forcibly limiting results to include only StackOverflow.
I really don't agree with this. If you depend on organic search to bring you users then:
a) you're at the will of the search engine's algorithm which can change at any time (like Google just did)
b) it means your users aren't the loyal type, and they will easily forget you
Take Reddit for example; If tommorow Google removes them from their index, I doubt much will change in terms of visitors since they have loyal users who know them by name.