They cite that they would loose their NCAA tournament money of about $250,000 per round they advance.

http://denver.sbnation.com/air-force-falcons/2012/3/26/29...

The story I read was that the merger as originally envisioned wasn't going to happen. The plan thats "not going to happen" would have seen the MWC and C-USA dissolve their respective conferences and reform as the new joint conference. The idea was that this would allow them to negate their current media contracts and negotiate new ones for more $$. Then it was pointed out to them that they'd forfeit their NCAA tournament shares by doing this. Though I didn't read the follow-up, that article (the Bret McMurphy article referenced in the SBNation article) suggested that they were just going to merge along more conventional lines and pass on renegotiating the media contracts.