Why and how did Aunt Polly decided to punish Tom?

There are several instances throughout the novel where Aunt Polly punishes Tom for his behavior.
Her most common form of punishment is beating Tom. In chapter 1, Aunt Polly attempts to beat him for hiding in the jam closet as she called for him. Later, she beats Tom for dropping the sugar bowl—even though Sid is the one responsible. During this incident, Polly justifies her actions, saying she punishes Tom because she loves him.
Polly does try other forms of punishment: one famous example is her forcing Tom to whitewash the fence instead of playing with his friends. Aunt Polly does this because she caught him sneaking in through the window the night before. However, Tom actually finds ways to manipulate the situation and gain enjoyment out of these kinds of punishments.
Later in the text, Polly even tries the guilt trip. After Sid tattles on Tom for sneaking out in the night, Polly tells her nephew he has “broken” her heart. This punishment works better than Aunt Polly’s other techniques, as Tom feels depressed at school for the rest of the day.
After discovering Tom is alive after his and the boys’ pirate adventure, Aunt Polly doesn’t even punish Tom at all. This suggests that all of Polly’s punishments truly have been the result of her love and care. She believes that discipline equals love (which is a Christian belief) and therefore tries her best to discipline the mischievous Tom in the ways she knows how.
The changes in Polly’s methods indicate Twain’s message about discipline: one has to understand the negative consequences of one’s actions on one’s own terms in order for any punishment to alter behavior.