I feel like you're overestimating the average person's interest and determination for a free and open internet...
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.