It's not about the Protocols over APIs. It's not even about open-web over walled-gardens.
Take a quick look back: Google Wave wasn't a safe bet, even though it was a federated protocol. On the other hand Facebook's Open Graph is a safe bet, even though it is hardly a protocol, but rather FB's API.
If you'd like to be sure something doesn't get deprecated, make sure it is widely adapted before you use it. In this case you would be a part of community, whose opinion has a leverage over technology providers.
But this way you may miss an early opportunity. It's all about choices. Luckily, we have plenty.
Take a quick look back: Google Wave wasn't a safe bet, even though it was a federated protocol. On the other hand Facebook's Open Graph is a safe bet, even though it is hardly a protocol, but rather FB's API.
If you'd like to be sure something doesn't get deprecated, make sure it is widely adapted before you use it. In this case you would be a part of community, whose opinion has a leverage over technology providers.
But this way you may miss an early opportunity. It's all about choices. Luckily, we have plenty.