Of course we want the Cowboys to win, regardless of circumstance. We're fans.
However, some cursory reseach has revealed an interesting trend. In 5 seasons since 1990, the Super Bowl has been a rematch of opponents that met in the regular season. In 4 of those 5 Super Bowl rematches, the winning team lost the regular season matchup against the same opponent.
In 2001, the Patriots beat the Rams in the Super Bowl, but lost to the Rams at home during the regular season.
In 1999, the Rams beat the Titans in the Super Bowl, but lost to the Titans on the road during the regular season.
In 1993, the Cowboys beat the Bills in the Super Bowl, but lost to the Bills at home during the regular season.
In 1990, the Giants beats the Bills in the Super Bowl, but lost to the Bills at home during the regular season.
The 1994 San Francisco 49ers are the only exception to this trend. They throttled the San Diego Chargers in the Super Bowl and during their regular season contest in San Diego.
In my opinion, the most surprising fact is how often the eventual Super Bowl champ lost at home.
Perhaps history will repeat itself?