Of course there's that element to it, but who would you rather piss off by leaving them out? Agger or Skrtel?
It doesn't just impact the individual players though. It also impacts the rest of the team. For example, why should Henderson bother working hard if he then thinks "well, Coutinho is getting in as soon as he's fit, so why should I bother trying?". So you have to, as a manager, always keep a keen eye on the bigger picture.
Would also assume that just because a player is in the team when it wins, that they've played an active part in that happening. I wouldn't attribute much (if any) credit to Skrtel for that WBA victory. I mean, he cleared that Anelka shot when it was him misjudging the ball that caused it. But other than that, how much did Skrtel earn us those 3 points?
Enough to keep the better suited Agger out of the team?
How many clearances and tackles did he make? What if he wasn't there to make them? What would have happened then? You can't downplay a player's contribution to a team win like that. Similarly, you can't overplay a player's contribution to a loss. It's a team game, and individuals have good individual games and bad individual games, but in the end, it's an organic, interlinked system. Every piece has a part to play.