Why does Silver call Captain Smollett a deserter?

Silver calls Smollett a deserter because of his presence with Jim, the Squire, and the others in the blockade. Silver notes that his presence in the blockade has marked him a deserter, and that as a result, the crew has chosen him (Silver) as their captain.

And then he turned again to the mutineers.

"And what do you want with your flag of truce?" he cried.

This time it was the other man who replied.

"Cap'n Silver, sir, to come on board and make terms," he shouted.

"Cap'n Silver! Don't know him. Who's he?" cried the captain. And we could hear him adding to himself, "Cap'n, is it? My heart, and here's promotion!"

Long John answered for himself. "Me, sir. These poor lads have chosen me cap'n, after your desertion, sir" - laying a particular emphasis upon the word "desertion." "We're willing to submit, if we can come to terms, and no bones about it. All I ask is your word, Cap'n Smollett, to let me safe and sound out of this here stockade, and one minute to get out o' shot before a gun is fired."