He waits like she signifies, because he's curious. There are a lot of assumptions he could make about Jyn Erso and her decline of his offer, but instead he chooses to just listen instead of preemptively analyzing. He's not plenty of other things to analyze.

Cassian makes a face, an agreeable sort of nod and curve of his mouth. "That's fair." He eats another bite of his food before continuing with no argument. He hates the idea of being fed by Imperial money, but it's not the first time. At least this bits of currency are going towards food and not violence. "But I don't really want to thank them for that, so I'll still say it to you instead."