I think Yamaha made that decision for him. And he really just didn't want to be sponsored by Gauloises/Altadis because they are the main competition for PM Europe/Marlboro, for whom he will be racing with in F1 next year.
First off- Yamaha decided to do this for ONE incredibly lame reason. Rossi's favorite color is yellow. The money the JTI is putting in will in effect be "like getting tips as sponsor money" as some DORNA offical put it. The biggest issue is how much is JTI going to have to pay Altadis for Yamaha's breach of contract. I'd almost bet that it's a wash in money. JTI is going to get Camel on the factory bikes in exchange for a one lump sum pay-off to Altadis to go away. The cost of running a top-tear MotoGP effort is now in the 10s of millions of dollars a year neighborhood. So, was it stupid to dump GO for Camel? Not for Rossi, who now gets to wear Yamaha Factory Yellow Race gear. Oh, and Colin looked pretty cool in Yamaha Yellow at Lagun, too. It's all gamesmenship at it's finest.
People should only be spokesmen for products they truly deeply belive in. For example, I know that I know that down to the bottom of his heart, Billy Dee Williams is a Colt 45 man, and always will be. Thus, in order to be sponsored by a tobacco company, a racer should have to drill a hole in his helmet and be smoking on the starting grid. Also, when he wins, he should mount the podium, affix the Majickal-ballcap-of-tire-manufacturing, then some umbrella girl should hand him an unopened pack of his favorite (i.e. the sponsors') smokes. he should open, take, light and drag deeply. then, and only then should he accept his trophy.
Yes, I am joking, but only a bit. Barry Sheene actually did both those things. And had perfectly healthy lungs till the day he died!