According to Box Office Mojo John Carter grossed $284 million with a production budget of $250 million. I know that many things are not included in the production budget, possibly advertising and distribution. Do those things account for so much money that grossing $34 million over the production budget just doesn't cut it?
It was considered a flop because it was supposed to be a bigger hit and a tent-pole to a new franchise. The production budget, like you opined, does not always cover advertising and distribution. When you spend $250 million, you expect your Domestic Total Gross to be well over $73 million. That is a flop. Even with world-wide BO it only made a small profit (not figuring in DVD sales). Put it another way: this $250 million movie is ranked 853rd in Domestic Box Office. That is not what they were hoping for.
It was a flop because it cost $307M and only grossed $284M. A substantial loss.