The official website says their motives are still unknown, and I doubt they'd do that right after CoroCoro confirms it, while showing a picture stating that very motive.
More likely, the people reporting on CoroCoro took the quote in that screenshot as a statement of their motives. "Oh, they think they can make money from fossil Pokemon? Confirmed that Team Flare's only motive is money." --- Socran's Razor: "Never attribute to massive stupidity by someone else, what could be explained by a tiny bit of stupidity on your own part."
Probably stealing stuff, sell them and black market dealings and such. They do look business-y. So basically, just for profit. --- Officially faved Ninetales everywhere, R - Burning Knight Executive http://pokefarm.org/_ext/user/Sephi#0