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I have asked myself that very question, many times. He's a grown man letting these two kids mess around with him, keeping him in a miserable shanty and torturing him with various-and unecessary-antics. He does complain quite a bit; but whenever he does, Tom lectures him about being a good and famous prisoner, and Jim ends up apologizing. Towards the end, he complains about all of it, get a lecture, and the book states, "Jim he was sorry, and said he wouldn't behave so no more." So, Jim is completely subservient and docile in his position, and takes it all. In the end, it causes him to actually get caught.
To really answer the question, we have to realize a few things about their society. Jim has spent his entire live as a slave, completely beholden to his masters, probably living in fear of what might happen if he goes against their will. He might have seen friends and family punished for going against a white person. And Tom is part of that entire mind-set. If you have spent your whole life following the will and orders of white people, it's hard to break that mold. Jim was probably afraid also that he would get caught. He was in the deep south, lost, and didn't have a plan. He had already been caught once, and was fearful of the repercussions of leaving. So, being a slave beholden to white people his entire life, being lost and disoriented, and being afraid of getting caught or lynched, might have kept him in that shed longer than some other person.