It is not the idea of the departments making more money, it is the idea that their actions to make more money have a negative affect on another university and their educational funds. The idea of the athletics being non-profit is that they are first and foremost an educational institution. It has been shown time and time again that educational values are not being put first and foremost during these conference realignments and thus would lead to the idea that education is not driving this bus, money is.
A corporation is a corporation, if you're better at marketing your corporation than I am and you do more business than me then there's nothing wrong with that, that's a free market. Same principle applies to non-profits. If a new organization springs up tomorrow that does a great job of marketing itself (even if it does a worse at the actual job) at disaster recovery, and as a result the red-cross brings in less and does less business then there's absolutely nothing wrong with that, congrats to the guys that made the new company.
As for whether education is driving conference re-alignment. A university could easily argue that the athletics department is a fund-raising arm of the university and that by partnering with other/different institutions it will be able to raise more money that it will actually add X Million dollars to the general university fund (like Texas, OSU and several other schools already do). In that sense, it's a business decision for the corporation that will help it succeed in educating even more students.
I guess I'm just trying to do is point out that the "threaten the tax-exempt argument" that alot of people seem to think is a slam dunk, isn't necessarily an easy win and that it is a weaker position than a lot of people seem to think if they think it will somehow save ISU athletics in the next 2 weeks as the dominoes start to fall.