Tom feels sorry for Aunt Polly as Aunt Polly believes him dead after he runs away. She has always chastised him for his bad behaviour but she genuinely cares about him.
Tom steals home secretly for one night from Jackson's Island where he is hiding out with Joe Harper and Huck Finn, and listens to Aunt Polly talking tearfully with Mrs Harper. Tom is deeply moved by her sorrow, as is clear in the following quote.
Aunt Polly knelt down and prayed for Tom so touchingly, so appealingly, and with such measureless love in her words and her old trembling voice, that he was weltering in tears again long before she was through (chapter 15).
When Aunt Polly finally falls asleep Tom kisses her softly and contemplates leaving her a note to reassure her that he's not dead after all. However he decides instead to make a surprise return to the town at the funeral which will be arranged for him and the other two boys in a few days' time.
Tom is shown to be a very mischievous and rather thoughtless boy, but he is also seen to have a good heart; he genuinely reciprocates his aunt's love.