There's very little substance to that article. All it says is that he can't kick everyone else out and run off with the tech. That doesn't mean he only bought in for the football or that he can't make money from developing and licensing the product.
If Berkshire Hathaway buys a 51% stake in an airline, Warren Buffett gets to steer as many of the business decisions as he wants. In practice, he usually has the good sense to let the people who know the business run the business, even when he owns the entire company. But he can overrule them if he wants. He could wake up one day and decide the airline would be better off leasing all of the planes to other airlines instead of flying them themselves. The minority shareholders might scream bloody murder, but they wouldn't be able to stop him.
Similarly, Dundon probably decided, over Polian and Ebersol's wishes, that there was a better way to make money off of the technology than by continuing to run the football league.
In the airline example, I suppose Buffett could also make the airline sell all of the planes to an entity he owns 100% for whatever price he feels is appropriate (lawsuits notwithstanding). But it sounds like there are mechanisms of some kind to prevent Dundon from doing something similar with the AAF's technology. Probably something like a transfer of ownership of the technology requires a supermajority of the voting shares or unanimous approval.
Maybe these guys legitimately wanted to build a feeder league for the NFL. They certainly got a good number of football guys on board. But what they're really betting on is the potential for the technology: Ebersol is on record as saying "we're a tech company that owns a football league." That tells me what their priorities really are, and as far as we know, the original owners still own 49% of the profits, losses, and capital transactions. They just needed a money guy to keep it afloat, and they put one in charge who has a different vision than they have.