Just like the MLB playoffs, NFL playoffs, etc.

Winning your conference should have some meaning.

The comparison to hoops is flawed, because there are 340+ D-I hoops teams, versus only 120 D-IA football schools.  Only around 18% of D-I hoops teams make the tournament.  Admittedly, 18% of 120 is 21.6 teams, so a 16-team playoff would be a little more difficult to break into than the NCAA basketball tournament, but not by a huge margin.

The teams that would be left out of a 16-team, 5 at-large bid playoff really wouldn't have a strong complaint.  For instance, this year you'd be looking at Stanford, Ohio State, Michigan State, Arkansas, and LSU as the at-larges, based on the BCS rankings.  Sure there are some decent teams left out, like Alabama, Oklahoma State, Missouri, and the Nebraska/Oklahoma loser, but that is the case each year in the NCAA basketball tournament as well, as some of the bubble teams that are left out would undoubtedly be able to beat some of the lower seeded teams.  Taking this year's hypothetical football tournament, each of the teams left out has 2+ losses, so they ultimately would only have themselves to blame for not qualifying for the tournament. 

Moreover, the inclusion of the non-BCS conferences helps give an advantage to the top ranked teams, increasing the significance of the regular season.  It is also essential for legal purposes.  Does the NCAA even run a national championship tournament in which the champion of every conference is not guaranteed a berth (not counting Ivy league football in FCS)? 

Finally, even if one assumes that the MAC is left out of a national football tournament, that isn't a sufficient reason not to have it.  We are already completely irrelevant in the current, horribly flawed system, so the worst thing that happens is that we remain irrelevant in a vastly improved system. 

With a possible 7-9 record they will yes but the point is that all conferences are not created equally.