Help students understand the characters by getting them to engage with them outside the text. One example of this kind of activity is known as "hot seating." Have the students take turns to select one of the characters from the text and let the others ask them questions. Limit the permissible answers to "Yes" and "No." Get the students to guess which of the characters the person is playing from the answers they give. If you feel the students are able enough, get them to choose another character and describe what they think of one of the other characters. Have the other students use this information to guess which role they are playing. As the teacher, you may have to take over the role of the character for this part.
Students can sometimes feel more empathy for the characters if they get to act out their roles and scenes. Split the students into groups and ask them to choose their favorite scene from the book. Get them to act the scene out for the other students. One way to develop this kind of activity is ask each student to write down their feelings and motivations in this section. This doesn't need to be especially complicated, you are simply trying to get them to understand that different characters will have different feelings within the scene. It is also good practice for literature assignments.
One of the pivotal events in the text is the boys' escape to the island for a life of piracy. Give the students the task of designing their own island. They can approach it practically. Looking at the particular challenges living on an island presents them with how they would overcome these obstacles. They can also approach the exercise artistically by looking at the feelings Tom and his friends have on the island and exploring how these feelings can be communicated in the way they draw, paint or model an island of their own.
One of the key themes in the book is the dropping of secrets, how it affects the keeper and others connected to it. Discuss the different secrets Tom keeps and reveals in the book. Then, get students to write a short account, real or fictional of keeping a secret, how it affects them and others. Get them to discuss the consequences of keeping and not keeping the secret and decide which is better in the end.