The US Military wanted to be an advertising sponsor of the NFL (just like an awful lot of other companies). They wanted a few concessions they felt would heighten the message they wanted to get out. The NFL accepted those concessions.

No scandal, no back room deals, no treachery. Just a completely above-board contract negotiation. No different than a company giving money to have their name put on the stadium...if you want my money, this is what I want in return.

No, the media didn't "cover" the story when the contract was reached just like they don't cover most advertising contracts. There just is absolutely nothing interesting or newsworthy about the contract until a player decided to use the national anthem as a protest stage.