He's pissed Goodell suspended his star running back... Erm, I mean, he feels Goodell has mishandled the anthem protest issue. Or the Ray Rice domestic violence issues. Or... something. Despite spearheading the effort to get him extended right up until Ezekiel Elliott got suspended.
Actually I think it's just about money. I don't think Jones wants to pay Goodell 49 million or whatever the hell they decided to pay him when the NFL isn't doing that great in the TV ratings. With Jones it ALL comes back to money. So perhaps he's a little pissed that the Cowboys won't sell a few tickets with Elliot out, but really it's more about how MUCH they are paying Goodell. It was fine when the money was rolling in, but with the ratings down, the bottom line could be impacted and Jone's sure doesn't want Goodell to be getting a larger portion of a shrinking income.