Why is Jem certain the Tom Robinson will be acquitted?

Jem is certain that the evidence that has been provided, in addition to his father's excellent defense, has left everyone without a doubt as to Tom's innocence.

Jem smiled. “He’s not supposed to lean, Reverend, but don’t fret, we’ve won it,” he said wisely. “Don’t see how any jury could convict on what we heard—”
“Now don’t you be so confident, Mr. Jem, I ain’t ever seen any jury decide in favor of a colored man over a white man…” But Jem took exception to Reverend Sykes, and we were subjected to a lengthy review of the evidence with Jem’s ideas on the law regarding rape: it wasn’t rape if she let you, but she had to be eighteen—in Alabama, that is—and Mayella was nineteen. Apparently you had to kick and holler, you had to be overpowered and stomped on, preferably knocked stone cold. If you were under eighteen, you didn’t have to go through all this.
“Mr. Jem,” Reverend Sykes demurred, “this ain’t a polite thing for little ladies to hear…”

No the answer is that Jem trusts the jury they will make the right decision but don't go as he thought.