Cunning and cleverness are major parts of Norse mythology – just consider the trickster god, Loki – so we aren't surprised that it plays a big part in the Norse-inspired Hobbit. At the same time, cunning seems to carry the implication of cruelty. Gollum is a cunning character because he constantly plots and plans, generally with evil intent. While Bilbo proves himself to be quite wily, what with his ring of invisibility and his handing over of the Arkenstone to Bard, his plots are always kindly meant. So his cleverness never has the cruel edge that distinguishes, say, Gollum's. Bilbo always tries to help other people who he has tricked, making him a pretty unusual burglar.
Bilbo's cleverness generally comes out in response to an immediate situation – for example, when Thorin and the dwarves are barricading themselves in the Lonely Mountain out of greed. He hasn't got the kind of global perspective that wise figures like Gandalf possess. But, in a sense, this makes his cleverness all the more extraordinary: he can't predict what will happen if he hands over the Arkenstone to Thorin's enemies the way Gandalf might, but Bilbo is always willing to take a chance if it will help other people.