The latter words come as a surprise to her. Not the compliment itself, necessarily, but the fact that Yondu moves on so quickly to trying to reassure her.

Even though Madoka is pretty sure that it can't be easy on Yondu either. He's nicer than he seems, and he must have gotten attached enough to Yoite if he was actually making something for the guy - so Madoka doesn't want to turn this into a pity party for herself. She can put on her big girl pants and be strong so she can try to comfort others instead.

"It's okay," she says, trying to make her voice sound as convincing as possible in this situation. (It's not quite there, but she's Trying.) "I've been on the train for so long now.. I've seen a lot of people leave by now."