Exactly, if you win your conference in the FCS you are in. They don't say "wellllllll, you see, the Soutland Conference is far superior to the Patriot Conference so why should the Patriot Conference get anyone in? They are just going to get crushed by the number one seed. So unless you conference is a certain level your teams should not even be considered because they are not the best of the best. And who did they play anyway?"
No, each conference, regardless of might unless bestowed upon them by ESPN, gets a shot to win it all. THAT is how it's supposed to work.
During the high times in the MWC there would have been a reasonable chance one of those teams sweep through the playoffs for a NC.