Tom probably thinks Mr.Weems is up to something strange like robing a bank or something.
Tom is a character who has always been overprotected. Because he was born with a terminal condition, his mother has always made sure that he is shielded from anything that could excite him, as it could prove fatal to him. However, this leads to Tom leading a boring, if safe, life. However, Mr. Weems gives Tom a second chance. He gives him a job and helps him become independent. It is likely that as Tom watches Mr. Weems leave for work, he is a little jealous of him. We can infer that Tom would want to have a regular life instead of one in which he is always protected.
