Er, no.
The reason the Colts "yards gained" is ranked low is because if you look at their "rushing play percentage" they consistently threw the ball more than other teams.
In 2006 they ranked 18th and 16th in yds/per attempt while ranking about that in attempts per game (18th).
Now in terms of attempts, in the year when they ranked worst for them, collectively, they attempted 5.6 fewer rushing attempts than the 10th rated team. Now that actually tells you something. They ran the ball. They just didn't get much out of it. They threw and played spotty defense and that, even in the hands of an all time great, will only take you so far. It's more surprising that they managed to get to and win a SB, let alone get to two.
As for the "average per gain" comparison, if you pick a any year, there's a little more than a 1 yard difference between the first team and the last team.
2010: leading 5.4 per carry, weakest, 3.6 per carry.
2008: leading 5.0 per carry, weakest, 3.4 per carry.
2004: leading 5.1 per carry, weakest, 3.5 per carry.
That said, this is a game of position and inches and a yard over three plays is huge in its impact.