Look at it this way, Swish3: We're playing on D1's dime. D1 football and men's basketball basically fund the entire organization.
D3 tournaments definitely do not break even, regardless of sport.
D1 football actually has nothing to do with this. NCAA makes NO money on big time D1 football. Those bowl games and the Bowl Championship Series money goes to the conferences and the schools - nothing goes to the NCAA. That's because it isn't an NCAA Championship. The NCAA may certify the games, but they don't see a penny. I've said for years, NCAA should punt D1 BCS and have nothing to do with it, because they get nothing from it (there are a lot of sports schools have that the NCAA doesn't have anything to do with).
If the NCAA was involved, it would be a traditional championship tournament like FBS.
The money basically comes from the D1 men's tournament primarily. There is some other money in other tournaments, but not much (the DI women's basketball tournament is essentially a trade-out with ESPN).
To Swish's point ... the "NCAA" in all avenues is the membership. DIII approves it's own rules. They decide how to best use their money. It is similar to what other sports and other divisions do, but DII does things different than DIII does with basketball, for example. Those in Indy just execute what DIII membership chooses to do.