People root for Tom because he is the main character, and played by Matt
Just watched this again after 15 years... Still an interesting movie and it brings memories.
Looking at Tom now. I think many (including me), rooted for Tom because the story is told through him and Matt Damon is a charming young guy. I don't think Dickie deserves to be murdered on the boat like that and no justice for Tom. Sure, Dickie was a jackass, a murderer according to his father, and a cheater. However, there was nothing wrong with getting annoyed by Tom. Tom was a nobody, a gay man who is delusional about Dickie, and wanted to stay in Dickie's lifestyle.
Tom almost walked away from a perfect crime. That was just too wonderful until he was trapped in a ship with Meredith and Peter. Killing Peter would prevent blowing off the cover... but was that really the best choice? How could he run away again when people find out his roommated is missing? Eventually the ship will dock and people would find out. It is equally risky for Tom to drag Peter's body out at night and dump it into the ocean.
Tom could have just told Meredith he is laying low with Peter, and ask her to pretend she never met him on the ship. Meredith would buy it, assuming Tom would take her out on a date again in the near future or something.
To me, he made the first mistake by telling Meredith he is Dickie. He should have known it was trouble after meeting her again in Rome, and found out she knew Freddie. Even thought it was the 50's. It's possible that somebody would have a photo of Dickie and Meredith would find out who's the real Dickie is. His relationship with Meredith would be over once she got back to the States anyway. Killing off Peter did very little to prolong the lies at that point.
Everything became a big mess and there was no way out. What a turn of events. He wanted the lifestyle, and he had a taste. He should have just savored what he had, and known his place. Just enjoy their last trip, go back to NYC and pocketed the $1000. The worst turn of the movie was Tom killing Freddie. What was he trying to accomplish? He couldn't pretend to be Dickie and live in that apartment forever.