The biggest answer is that the prestige of your team vs. the prestige of the team you're applying to has nothing to do with the jobs process.
Think of it this way: You and I have identical resumes and both take over programs at the same time. I take over an A+ program, you take over a D program. Four seasons later, I've sucked up the joing and am down to a B+; you've kicked butt and are up to a C+. Should the fact that I coach a B+ make me more qualified for a job despite the fact that you've clearly outperformed me? Of course not.
So what actually matters is your resume, not the prestige of your program. And while you've done a nice job at Loyola, it's in a weak conference, you haven't won a NT game, and have had an RPI better than 98 only once. And perhaps even more important in this instance, you don't have a real deep breadth of experience -- four total seasons at DI, and never past the NT 2nd round even in D2/D3. Simply put, that's just not going to get a BCS job, even at a program that has fallen on hard times.