You don't have to be a rocket scientist to know that one of the Rays major problems on the field is pitching. The Rays ranked third worst in 2006 in Runs/Allowed per game 5.28.
Defensive Efficiency Ratio measures the percentage of times balls in play are turned into outs by the team's fielders, not including homeruns. The Rays had a DER that hovers around 68%.
The biggest defensive deficiency the Devil Rays had, according to the Hardball Times, was when balls were put onto the ground. Fielding problems were balls on ground -82.
Pinto uses play-by-play data to determine the probability of a ball in play being converted to an out based on six parameters: Direction of hit (a vector), The type of hit (Fly, ground, line drive, bunt), How hard the ball was hit (slow, medium, hard), The park, The handedness of the pitcher, The handedness of the batter.
PMR in 2006 supports that the Rays problem was infield defense.
Cantu , Huff, and Wigginton seem to be where the problem lies.
Toby Hall and Navarro were stellar.
As were Lugo and Zobrist.