Sports has been the undoing of US education in schools  earlier and now it seems even in higher ed.
The sooner they get rid of sports from educational institutes the better for them.
Also, The Atlantic is not a reliable source. It prints garbage like this:
"Football at Premont cost about $1,300 a player. Math, by contrast, cost just $618 a student."
even though everyone at the school takes math, very few play football, and not everyone involved in football is a player.
Atlantic may or may not be a reliable source. What about this? A coach is given a whooping $7,004,000 salary.
Michigan head coach Jim Harbaugh is in his first year with the Wolverines and sits behind Saban with a $7,004,000 total pay. 
On the wider scale, extracurriculars only affect share-of-students rather than increase the total number of students, so such programs have a globally negative ROI. But each individual university is making a rational decision.
 I'm assuming there's a negligible percentage of students that would avoid college entirely if no or very few colleges had football programs. It's safe to ignore football scholarships, because you still have the option of giving the students free money, which is cheaper than giving them free money and also running a football program.
 I'm also assuming the football program itself doesn't generate enough revenue to offset its costs, and only affects enrollment. I honestly don't know if they make enough money in tickets and trinkets to offset the debt service for a stadium, salaries for coaches, free tuition for students, etc. If the ROI is positive(or even negative, but with a positive cap rate), then it might be rational economically to continue them.