Captain Smollett has a number of grievances he wishes to share with Squire Trelawney. For one thing, he feels like he's been left in the dark as to the Hispaniola's mission. Moreover, when Trelawney hired the crew, he placed way too much faith in Long John Silver. Thanks to this error of judgement on the Squire's part, the good ship Hispaniola is now infested with pirates. Smollett bluntly tells Trelawney that the doesn't like these men—and who can blame him? As well as being a murderous band of cutthroats, they owe their loyalty to Silver, not Smollett. Smollett is genuinely concerned that Silver's scurvy crew will stage a mutiny on the high seas.
In due course, Smollett will come to change his mind once the ship has safely reached the island, but for now he's not very happy at all. Although Trelawney—with a little help from Silver—hired the crew, it's still Smollett's ship, and he doesn't take too kindly to having his authority as captain undermined, whether it's by a respectable gentleman like Squire Trelawney or a notorious pirate like Long John Silver.