You're way too smart to not see the serious flaw in this line of reasoning.
You say it makes sense for the pundits to question the conference when the team they expect to win said conference loses to a I-AA. That holds true ONLY if it makes sense for the pundits to continue to hold their belief that the team in question is one of the conference's best after said loss. In other words, it makes sense for the pundits to assume they are right about Michigan in the face of overwhelming evidence to the contrary. It makes sense to question people/teams that have nothing to do with the program that is swirling around the drain rather than to question your own prognosticating skills.
We can understand why they think that way. Arrogance is not a weakness confined to sports media types. But saying that this line of reasoning makes sense is beneath you.