They weren't all missing but one or the other were. Had they all been fit then he wouldn't have started. He's played plenty of games with both Torres and Gerrard (and Masch too) in the same side but he's not played well enough.
At the start of the season i would have said that Keane's competing with Alonso for his place in the side as Torres, Gerrard and Masch's form over the last season had secured their places. Keane would have been foolish to think he'd be a certain starter and he's even more foolish if he thinks that the way he's been playing will secure his place.
With Alonso being arguably our best player this season and Torres, Masch and Gerrard all back then Keane's just going to have to work hard and take his chances, just like every other player.
You're right Rafa's man management is poor. He takes a hands off approach with the players and leaves that stuff to his coaches. No doubt Sammy Lee would have been the man to tell Keane just like he'd have been the one who told Benayoun or Babel when they've been left out of the squad too.
No he's a squad player not a bench warmer. A bench warmer wouldn't have played 27 games, starting 23 of those.
You're right about Rafa often taking strikers off for midfielders though, he didn't 'constantly' sub Torres though

Rafa's idea is (whether you agree or not) that if the team's not creating chances then the system needs to change rather than the strikers. The fact that we're far more effective playing a 4-2-3-1 than a 4-4-2 would be another reason that Keane (or Kuyt/Crouch last season) will be taken off for a midfielder.