What on earth do you base this on?
If you want to say that in a given year one of the top FCS teams playing in a game that means the world to them could and sometimes will beat one of that year's worst BCS teams playing in a game that means almost nothing to them, than yes I'll agree.
In a vacuum does our program run better than the bottom feeding BCS teams? No doubt about it. But the ingrained advantages that even the worst major-conference programs have can't be ignored for our own convenience.