It totally makes sense that Tom is the protagonist because he’s the one telling the story and the narrator is almost always the protagonist. We get his thoughts and we see his character sympathetically.
The protagonist has to be Amanda because in the classic plot of a tragedy, she fulfills the role of committing to a dream and then having that dream completely squashed.
Doubtlessly, the protagonist is Laura. She’s the only one that, we, the audience, don’t get annoyed with all the time or feel the need to judge on the basis of his/her awful moral decisions, and she has all these great protagonist qualities like being perceptive and kind and beautiful. She even has the fatal flaw built in, what with the shyness and all.