The definition and notions of "profitable" in college athletics is intentionally elusive and varies wildly. Both sides abuse this obfuscation to their advantage, and the articles you link to, besides being archaic, are some of the worst abuses I've seen on this topic.
Each state, university, have different requirements on what is reported as subsidies. For example, discounting an out of state athlete's tuition may or may not be a subsidy. In some schools, all of the apparel sold with a school logo is athletics money, while in others, a percentage. And of course, private universities like Stanford, Northwestern, and the Ivys report very little.
The articles also strawman the entire argument by using student fees to fund athletics. True, some schools abuse the hell out of them. Some Division III schools have ungodly amounts of athletic fees, and the students will never see their return. However, success in athletics, and football in particular, add to the brand of the school. Anti-athletics faculty love to huff and puff about how this isn't true, but common sense and studies in business schools routinely dispute this. Boston College reported a 3x increase in enrollment the year after Doug Flutie threw his touchdown. University of Alabama's enrollment has gone way up while the acceptance rate has gone way down in Nick Saban's tenure. Even if you never attend a game of any sort in school, you will gain in the perceived value of your degree.
> I haven't looked into it but I doubt any football program paid for the stadium they use
This tells me all I need to know about your bias on this.