Dean is losing faith pretty much in everything lately. The necklace was a sentimental gift for Dean because Sam gave it to him instead of their father. So Dean feels like it's, along other things, the symbol of him being more than a brother to Sam, almost a father so when Castiel says that the necklace is worthless Dean kept it really bad and being all broke as he is, he threw it away... BUT, Jensen said, SAM WAS STILL IN THE ROOM WHEN DEAN GETS OUT OF THE MOTEL ROOM SO.... WHO KNOWS? ;D *winks*
I'm telling you, my amount of worry for that amulet is not healthy. I should write to the writers and tell them what a fantastic job they've done coming up with a tangible symbol of the brotherly-bond, because the idea of them losing that amulet is making me feel like someone just killed my puppy...or my first-born.