The implication of the original posters mention of his district's "fully funded" team was definitely not that it was turning a profit... but that the school is instead still spending on it while cutting services like the library.

Why would he complain, in this context, about a football program that is generating income for the district?

Yes, that's exactly the implication I'm challenging. The amount of times I've heard the "they're cutting thing-i-think-is-important but keeping the football program" but who don't know that it's because the football program is self-sustaining is so frustrating. They're not choosing football over music or art or whatever. For sports which aren't local cash-cows the parents are having to buy the new equipment and uniforms. Sadly, no one stepped up for the music program like that.