Two thoughts:
There is a SOS element to the computer polls, and human voters also consider schedule played.
Also, there's a reason Atlantic Coast, Big East, Big Ten, Big 12, Pac-12, and SEC conferences have automatic berths, whereas Conference USA, the Mid-American Conference, the Mountain West Conference, the Sun Belt Conference, or the Western Athletic Conference have to earn berths through rankings/polls.
Bottom line, it all comes down to wins and losses and the top 2 teams appear in the NC game. (unless you play in Mid-Am, MWC, Sun or WAC).
So, who is actually being penalized?
No team winning the majority of that gauntlet gets penalized. Win the your conference and go BCS'in. Win them all and have a very good chance at going to the NC (unless you play in Mid-Am, MWC, Sun or WAC). .
BCS has BSU at #4. We've been through this already. BSU pounded an SEC team by 14 points and that same SEC team is 4-1 in conference play. They also beat Toledo and Tulsa, who are currently undefeated in conference play.