From what I gather from reading the Oculus forums, the intention is for FB to have a central VR Portal with an app store, support, etc and plaster that with ads, being how they recoup their investment.
There is no intention to make this the exclusive content site (so you could still make a mod for a game, or run a game with native support without ever needing to visit the portal) and having it insert popup ads in existing games is just beyond retarded.
But yes, I agree it has completely killed the part of me that was excited to see it succeed because it was from an indie developer.