Basically conferences = divisions in the NFL
Each division champ gets in because those teams have the most similar schedule even though schedules are even unbalanced in your division. It's the fair way to do it, each division champ gets the chance to prove themselves on the field plus now 3 at large from each the NFC and AFC.
Yeah we can say the SEC and Big Ten are the strongest due to a couple of non-conference games but we really don't know, it's mostly an assumption. That's why it's the most fair to have conference champs auto qualify.