Allowing such proprietary networks to run over public radio spectrum causes harm to the real internet - and not just by slowing it down and making it more expensive.
The main long-term harm is the stifling effect on innovation, especially in businesses that rely on network effects: Even if you are a regular internet user, but some of your friends are on internet.org, you can only use communication, collaboration or social networking apps that are on internet.org. Even in other categories of apps, you might only hear about those that are on internet.org.
This means that we will move from an economy where end users decide which apps get popular, to one where facebook picks the winners.
This is scary.
But before internet.org, you couldn't even communicate with them.