Sam hadn't expected that reaction. Pretty much at all. He'd expected...well, he didn't really know what he'd expected. But he'd known that it wasn't that. He didn't say anything immediately, mostly because he had no idea what to say in a situation like this.
Judas was upset, or angry or something. Sam wanted to say that he understood why, but the fact of the matter was that he probably had no idea. It could be for any number of reasons and they were all definitely plausible. He was almost better off not saying anything. Still, for invoking that kind of reaction, he definitely felt like something needed to be said.
"I'm sorry I told you," he replied with, squirming a little in his seat.
It wasn't that he thought that the guy would hurt him - though now that he thought about it, it wasn't a totally implausible concept. But, being a Winchester, he was always uncomfortable in confrontational situations.