It's actually not because ND isn't in a conference, it's that they are NOT in BCS conference. A top 6 team from a non-BCS conference gets an automatic bid. Hence the reason #6 Utah was in a BCS game last year and #5 Cal wasn't, which is basically the exact same situation as this year. So this might be a "Notre Dame Rule" but it benefits other teams as well.

Two years in a row a #6 team gets the auto bid while the #5 team didn't. Seems like a system that only something as idiotic as the BCS could come up with