No doubt that is the case! There is definitely a bias toward the Power 5. And unfortunately, because of how much money is involved in college football and the fact that the season can’t realistically be extended, there is no easy answer.
Of course there is an easy answer. Run DI football the way every other NCAA sport runs. AQs for all conference champions and a few wildcards to round out a field. There are 10 FBS conferences. So a 12 team tournament would be fine. Mandate an 11 game regular season, 1 more than DIII or DII I believe, then have a 4 round tournament. The top 4 teams would get a bye, 5 would play 12, etc. In that first round, 7vs10, 8 vs9 should be good games, but basically the first 6 teams either get a bye or a simple opponent. A reward for a good season but it gives every FBS team a chance at the beginning of the season to be champion, which is exactly what we don't have now.
With 1 week less in the season, the first round could be played on Conference Championship weekend, you'd have 4 games and play them at the higher seeded team. Same with the second round Army-Navy Weekend. Another 4 games at the higher seeded team. The last 2 rounds could be done like they do it now. No extension to the season, the same number of games for any of the top 4 seeds winning the title (3 playoff games vs 2, but 1 fewer during the season), and only a 1 game extension for any of the lower seeds. The DIII National Champion plays 15 games, but somehow DI kids can't?
Only DI football has no NCAA championship, and that's why I don't care if UCF claims one, or Auburn claims one from 2004, or Utah from 2008 or any other undefeated team. Because there is no official NCAA championship and never has been thanks to the conferences and bowl system. There are AP champions, Coach's Poll Champions, BCS Champions, CFP Champions... but no NCAA champions. Until that is fixed, I have no problems with a variety of teams claiming an undefeated season as a National Title. Better than some of the joke titles schools like Alabama have claimed in the past.