According to Dave Meltzer on Wrestling Observer Radio, John Cena's injury at the hands of Drew Mcintyre on last Monday's Raw is indeed a storyline, and he was always set to be "injured" and miss the Royal Rumble event due to filming commitment.
The injury storyline was meant to be that NXT call-up Lars Sullivan injured Cena in his Raw debut and then this would lead to a WrestleMania match, but Sullivan has yet to make his main roster debut due to anxiety.
"I was under the impression that John Cena was going to start doing a movie on Sunday so he wasn’t going to be at the Royal Rumble" said Meltzer.
He added on Lars Sullivan, "my impression is that Lars Sullivan was supposed to injure him and that didn’t happen so they created an injury and he’s not going to be in the Royal Rumble." before confirming Cena is not really injured John Cena’s injury is a work though."