I was thinking something similar last night, although a little differently. Why do schools offer non-revenue generating sports, such as track, lacrosse, etc?
If you focus on athletic scholarships in college, the justification is Title IX, which requires school sports, including financial support for these sports, to be evenly divided between men and women (or boys and girls).
To offer scholarships for college football, the same school must field a female team(s) and offer the same number of scholarships.
The trend I have seen on the high school and junior college level is to eliminate the non-revenue sports or perhaps all sports all-together. (See St. Louis Community College for one such example.)
While Division I, II, & III Track and Field and Cross Country are well-established, I can ultimately see these sports follow the high school route of turning all sports into independent (of the school) club sports.
Even in track, you see the two or three best kids quit college early to pursue their pro career. With the college bubble about to burst, I see promising high school kids choosing cities instead of colleges to continue their running careers. Look at the Team Rogue Local Elite Team in Austin -
http://www.roguerunning.com/news/588.html
. If you're a guy who can run 16:10, you get $1000 in free merchandise and 30% off after that.
So to answer your question and to recap my opinion, the justification is that universities want to keep their revenue-generating sports and Title IX makes them offer and fund the other sports.
But eventually the NCAA monopoly will have to cave and schools will be forced to share revenue with the basketball and football players. Then the sports programs at every school will be a losing proposition. You'll see more expensive sports drop by the wayside. And eventually I think we'll see a future where running (especially track and field) will be dominated by clubs at the high school, college, and post-collegiate levels.