Actually I think it is fair. Plenty of teams have made the playoffs because they won their division even though they weren't very good. Win-loss records can sometimes be deceiving. Witness the Cardinals last year almost not making the World Series despite winning 105 games, nearly beaten in the NLCS by an Astros team that got hot at the end of the year. Or the 2003 Giants, who must have been the most overrated 100-win team of all time, getting spanked by the Marlins in the first round. And then there are all those 100-win Braves teams since 1991 (six, including three in a row), none of which won the World Series.
This is a great argument for the wild card. At least four wild card teams have won the World Series, and at least two others made it there. (Could be more, just off the top of my head.) I can't think of a single team that made the playoffs via the wild card that wasn't at least a very good team. In most years there's a wild card team that's better than one of the division winners, making it that much more unlikely that a crappy team will win the World Series.
"Not fair" describes the plight of the Blue Jays, Orioles, and Devil Rays. These three teams are unfortunate enough to be in the same division as the two highest spending teams in baseball, who can make up for bad decisions by throwing more money around. If the three-division wild card system yields a half dozen really, really good wild card teams and one pathetic division winner in each decade, then I'd say it's doing a good job.