The internet is young. Open source and permanent beta is the future of the internet, not tight API and shitty marketing schemes. There will come a time when everyone grows up with, not just the internet's presence, but also a deeper understanding of the internet that can only come with it having permeated your life since you were born. We think the internet is a lifestyle, but it's not yet; not even close. And when it is, this sort of thing won't be tolerated -- that's just economics.
Agreed. The internet feels much more silo-ed than today than years ago. I think quality search is a huge part of it. When the means of navigating is monopolized and users have mostly one point of entry, they only step into those SEO constructed rooms that branch off from that one door. A few large platforms penetrate the consciousness outside of the main doorway (most brink their walled garden with them). I think there is more interesting stuff than there ever has been, but our points of entry have taken over and behaviorally shielded us from it. I think a lot of the curiosa of the early web was enabled by shitty indexing and search. It's still all there though, but the vast majority of users have no idea.
I completely agree with you that the internet is going to become ingrained in people's lives in ways we can't even think of. What I don't agree with is that people will start to care more about "protecting freedom" or anything like that. When everyone grows up with the internet it'll be easy for them to take it for granted. It'll seem like just another part of life to them. Sure you'll get the fringe people who care deeply about keeping the internet "good" and "real" but they'll just be fringe people like always.
It's not about protecting freedoms, it's about supply and demand (I think). Is Facebook made better or worse with the app discussed in the article? Better. Over enough time, the customizable option will win out. On a large scale, I think this means websites and internet companies in the future will be extremely cognizant of user feedback. Look at the add-on market, the iPhone app market, etc. Those barely existed 3-4 years ago when compared to today.