Participation on internet.org is subject to approval by Facebook and ISPs. They choose the winners on their platform, not end users.
Imagine a world where, say, 20% of users are on internet.org. If you're building a consumer service that benefits from network effects, you must be on internet.org or else you will be eaten up by a competitor who is. Facebook, through its veto over internet.org participation, can now play an outsize role in deciding which consumer internet services get traction and which don’t.
App developers will divert resources from building features that users want, into building features that gets them perks from Facebook — probably by pushing more and more user data into the “open” graph. This would not just harm internet.org consumers, it will harm every internet user.