I've often wondered about this, not only at the FCS level, but at the non P5 FBS levels as well. Most of those conferences have a pretty large geographic footprint. Travel costs are static regardless of the level you're playing at, but schools like NDSU or New Mexico State aren't bringing in BTN type TV revenue, or drawing 50-100k fans to games for gate receipts. How can they possibly not lose a ton of money?
Cost of scholarships is an interesting topic - this came up on Reusse's show last week. UMD is not renewing their women's hockey coach's contract because the program is hemmoraging money, despite being one of the top schools in the sport. A big reason for the success, and high cost of the program is that most of the players are from Canada or Europe. UMD has to value those scholarships on the books at the full cost of international student tuition which is a huge financial burden to the program. I didn't realize this, but it makes sense. Not sure if this is the case with all schools, but it would explain why NDSU recruits so heavily in Minnesota where there's a tuition reciprocity agreement. Smaller schools in states with little talent, like New Mexico are going to have to accept higher financial costs on the books for scholarship athletes and that too has to hurt.
I've thought for a long time that D2 football could be in trouble, or at least merge with or take on the non-scholarship model with D3. I have a hard time seeing where St. Cloud/Mankato/Moorhead etc. can justify keeping scholarship football when interest is low and costs are high. I think it would make a ton of sense for the biggest three NSIC schools (Mankato, St. Cloud and Duluth) to go the route of UN-Omaha and drop football and move to D1 for all other sports. You cut the the money drain that is football, and gain the possibility of payouts should you make it to the big dance every ten years or so.