From the beginning, Captain Smollett is suspicious the crew hired for the adventure. He appears perpetually angry to Jim Hawkins, and both Jim and the reader quickly learn this is due to the man's suspicions. He dislikes knowing less about what they are doing than anyone else on board the ship, since he is supposed to be the captain of the crew. He also does not like the character of the crew members (for example, he thinks Mr. Arrow is too "familiar" with the other sailors, despite being in a position of authority).
Captain Smollett is the opposite of Long John Silver and his crew of pirates. He is disciplined, stern, and, initially to a young boy like Jim Hawkins, perfectly square. Jim even resents Smollett a bit, believing he is unfairly prejudiced against Long John Silver. Squire Trelawney shares Jim's anger at Smollett, even going as far as to argue that Smollett must be prejudiced against the ship. It is only once the crew of the Hispaniola actually proves mutinous and murderous that Jim realizes Smollett was in the right all along. From that point on, he regards him as an ally, not the impediment to the adventure he believed him to be.