Why does he later apologize to Jem after Mr. Macey's comment?

Silas apologizes because he accused Jem without a witness, and he was rash is his accusation.

"I was wrong," he said—"yes, yes—I ought to have thought. There's nothing to witness against you, Jem. Only you'd been into my house oftener than anybody else, and so you came into my head. I don't accuse you—I won't accuse anybody—only," he added, lifting up his hands to his head, and turning away with bewildered misery, "I try—I try to think where my guineas can be."