I agree strongly with gretzky. The way fantasy is now, it rewards owners who have a strong knowledge of all of baseball and not just players. Not only do you have to know that Derrek Lee is a good player, but that he moved from a big running team to the Cubs, where he might hit more homers but will almost certainly not have as many chances to steal. Wins work the same way--not only do you have to know that Jake Peavy is a talented young pitcher, but if you correctly predict that the Padres are going to have a strong offense this year, you will do better in wins.
In short, stats like this make knowledge more important to fantasy success.
Regardless of that, though, I think wins aren't so unfair of a stat. To make a bizarre cross-sport analogy, I played tennis for four years in high school, and there was one player on the team that always played just well enough to lose a close match. He would lose 7-5, 7-5 no matter whether we were playing the best team in the state or the worst. I, myself, played tons of long, close matches, but never lost a conference match (not to toot my own horn, or anything). In short, I guess he was a choke artist, but that's not really the point. I think it translates to fantasy baseball in that some pitchers will pitch better in close games and some will flop.
Granted, it still often comes down to run support, but not necessarily to the extent that everyone says. Sure, Pettite wouldn't have gotten 6 runs of support in a given game if he'd played for the Tigers--but maybe if he played for the Tigers he would have born down and held the other team to 2 instead of 4 and gotten the win anyway. A lot of times, pitchers with a big lead will ease up and just try to get through innings, leading to higher ERAs while still getting the win.
That was a lot of words for a fairly simple point, but I would say that some pitchers are winners, and will pitch just as well as they have to. Wins are by no means a perfect category, but they do measure this factor--and I think they make the game fun. You don't just root for your pitcher to do well, you root for his team to score, and you get more involved in the game.