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Tom is "a large, friendly-looking rat wearing a spotted handkerchief around his head" (15.26), and can talk, too. Kipper, his human buddy, refers to him as "'the brains of this outfit'" (15.33), and indeed, Tom does do a lot of the talking and dealing.
He's clever enough to pretend to be a dog and bite the leg of a "horse" (one of Snatcher's human mounts for the cheese hunt) in order to create a distraction for Arthur to sneak into the Cheese Hall. But he also thinks it's okay for Arthur to try to access the enemy's home base alone, so maybe we wouldn't leave our kids with him. When Willbury takes him to task for this, Tom at least ends up looking "even guiltier" (24.6), showing that he knows maybe it wasn't the best idea, and he's totally capable of remorse.
Tom's braininess makes him perfect for certain tasks, like manipulating the doll-communicator contraption that Grandfather has rigged to get the prison cell keys to Arthur. He's also the first one to recognize Framley in his monstrous new form. So it makes sense when Tom's voted captain at the end of the story, though he complains that he "'can't stand the paperwork'" (55.13). Maybe Tom's too brainy to be bogged down with so much bureaucratic stuff.