1) Per Death to the BCS, there are quite a few teams that lose money or at best, break even. Furthermore, the only reason that many even break even are due to the distributions from conference revenue. For instance, one of the years that Florida won the national title, the book stated that something along the lines of 80% of the SEC's bowl teams would have turned in a loss for their bowl trip if it weren't for Florida's big cut. In fact, after Florida had to share all that money, they barely turned a profit themselves. Now, they're just talking about the postseason here, but nevertheless, it's not surprising to me after reading that book that there are so few departments that actually make money. The big moneymakers in college football are the coaches, ADs, and bowl execs.
2) Both college athletic departments and the bowls remain tax exempt by being considered non-profit organizations. I'm not going to act like I know all the details of that, but they obviously have to be very careful about how income is reported and where it's going. My point is that just because a department is reporting a loss or small gain, I have a feeling that it could easily be partly due to them funding a "money for a rainy day" account at the same time.