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Why? Well, golly, if the University of Northern Iowa (UNI) gets almost $1 million in guarantees for playing Iowa and Wisconsin, and their football budget is only $3.3 million, then that's one-third of their football budget! Nobody can take such a hit.
There are (at least) two problems with this view. The first is identified by turning to the data on FBS-FCS match ups (as opposed to the hand-wringing of the UNI athletic director, Troy Dannen, quoted in Jason Belser's Forbes SportsMoney piece that inspired the title for this post).
There are 124 FBS programs. 81% of them (101 programs) played an FCS opponent last season. That ends up to be 82 of the total 127 FCS programs that played in such a game (26 of these played in more than one FBS game; the whipping boy champ was Nicholls State that played in 3--Oregon State in the Pac-12, Tulsa in C-USA, and Southern Alabama in the Sun Belt). Now, just these data make it look like quite a large proportion of FCS programs earn these whipping boy pay days.
But only a portion of these games were against FBS opponents that paid in the hundreds of thousands of dollars (I'm sure that the MAC's Kent State didn't pay much to Towson, for example). Let's look at FCS programs that played, as did UNI, only for the type of pay day under discussion, that is, against the Big 6 (ACC, Big 12, Big Ten, Pac 12, SEC, and, well, to be more charitable than the lords of the FBS post-season, the Big East). That would be 57 of the 127 FCS programs. So, as I jested above, "Nobody can take such a hit" except for the 55% of FCS schools that never get this type of game in the first place! [By the way, if you throw out the Big East, as has the now Big Five that run the FBS post-season, the number falls by 9 more FCS schools, down to 48.]
Somehow, fully 70 FCS programs seem to get along quite nicely without taking a Big Time bruising (including FCS Champion North Dakota State). [By the way, the ACC and the SEC are the only two FBS conferences where every member played at least once against an FCS opponent; the 23 FBS programs that left the FCS off their schedule include Texas, UConn, Ohio State, Penn State, Michigan, Michigan State, Stanford, UCLA, and Southern Cal in the Big 6; but the list also includes Troy, Boise State, and Rice to name a few.]
And that brings me to the second problem with this view. Why in the Wide World of Sports would anybody believe that these "bonus" payments go only to fund the football program? According to the most recent OPE data (2011-12), the UNI athletic department spent $11.4 million on all of its sports operations and total athletic department spending was $14.6 million. AD Dannen is surely on top of his game and has already set the football program to maximize revenue, allowing for the fact that these bonus days are stochastic; if he doesn't get them anymore, then he revises his athletic department budget, not his football budget only. While $1 million out of $14.6 would be missed, 7% is a manageable reduction. Again, 70 other FCS programs seem to operate at that level quite nicely, thank you.
If anything, the real plum for FCS ADs is the chance, albeit small, that their team upsets their FBS host. Michigan fans still cringe at the mention of Appy State. And, if anything, the slight reduction in the quality of just those top FCS programs that get an FBS game or two would enhance balance across the FCS. Without that extra bonus, more of the FCS is in the market for the top FCS coaches, like FCS Coach of the Year Willie Fritz whose Sam Houston State Bearkats fell short in the FCS championship game against North Dakota State--the Bearkats played both Baylor and Texas A&M this last season.