At first, Mr. Pluto is an antagonist; he doesn't want Thomas and his family on the Dies Drear property, because he's worried they might reveal his secrets. However, when he realizes that the Smalls are trustworthy, Mr. Pluto teams up with them against the real antagonists, the Darrows.
The Darrows are the real antagonists of the story. They terrorize (antagonize) the Smalls and Mr. Pluto so they can try to find the treasure of Dies Drear. Of course, not all the Darrows are antagonists. Even though Thomas thinks Mac Darrow is out to get him at first, he learns that Mac was actually slapped by his brothers when he said he wanted to be Thomas's friend.