The Rose Bowl's only obligation is to take the conference winners from the Pac-12 and the Big 10. If one or both of those teams are unavailable, the Rose Bowl is free to take who ever else is available. The Rose Bowl said in November that they would use the next highest ranked team in the playoff poll from the conference to replace a conference champsion, which happened to be USC. The Rose Bowl also said they would not necessarily use this same criteria in the future. They may change it.
You can't blame the Rose Bowl for wanting to put together the best possible matchup to maximize ratings and national attention.