The NCAA does not have to comply with Title IX so there is no argument whatsoever here. Title IX is part of the Educational Ammendment of 1972. Only SCHOOLS receiving federal funding have to comply with Title IX. Not only is the NCAA not an educational institution, but they also do not receive federal funding. There isn't any discrimination here, but even if there were you should not blame Title IX. Any discrimination here would be the NCAA doing it because it wants to, not because they have to or someone told them to.
Additionally, it is very rare for a football program to be making money. Only the huge football schools such as Ohio State, Michigan, USC, Florida St., etc would you see a profit. Do the math of how much it costs for 85 full scholarships, equipment and uniforms for those 85 plus walk-ons, facilities and facility maintenance(stadium, weight room, etc.), coaching salaries(head coach and however many paid assistants-usually way too many), athletic trainers and training equipment, transportation, accomodation(hotels for the away games, but also the home games-many schools put their kids up in a hotel for home games for minimal distractions), and all other miscellaneous costs including those I forgot to mention. It is just a big myth that football programs make a profit and fund the other programs.