That article is specifically only looking at public school employees, so many schools aren't being considered.

Just in the Big 12 alone, though, you've got the following:

Kansas: Lance Leipold ($7.8 million) vs. Bill Self ($9.6 million)
Houston: Willie Fritz ($4.5 million) vs. Kelvin Sampson ($4.6 million)
Arizona: Brent Brennan ($2.7 million) vs. Tommy Lloyd ($4.1 million)
Baylor: Dave Aranda ($3 million) vs. Scott Drew ($5.1 million)
BYU: Kalani Sitake ($3 million) vs. Kevin Young ($4.3 million)

Yes, those also happen to be the 5 highest paid basketball coaches in the (new) conference, but that's 5 of the 16 teams in the Big 12 that are currently paying their basketball coaches more than their football coaches - which is far from the claim of 3 teams in the country that are doing so.

Also, if and when Kalani Sitake's contract is up for renegotiation (or he gets fired), I'd assume BYU would try and be more competitive in their salary offering (somewhere in the $4.5-5 million range). If they don't then it's a signal to me that they aren't willing to invest in football like they need to.