NIU beating a team like ND doesn't happen "all of the time," (I shouldn't have said that) but it does happen occasionally. They're not literally invincible. But a playoff that included all of the conference champions in FBS would be far less interesting and competitive than March Madness, which is basically the only example of a collegiate tournament that is "thriving" in the sense that that word means with regard to major college football. Because those teams would rarely, if ever, have the ability to upset a top team because of the structural differences between football and basketball.