And not to mention, even Ellie touches on this before
and after this event takes place too. She said that Tommy and Joel had to do a lot of things in order to survive, and they never really address it in the first game, but it was always implied that Joel did some pretty dark shyt after Sarah died. So in a world like that and your hands being that bloody, it makes absolute sense that he'd have some people wanting his head.
In fact in the first game, you had those cannibals looking for Joel and Ellie. And seeing as how Joel wiped out an entire Firefly hospital in order to save Ellie... Yeah, dude is probably on the top of many people's shyt lists.
It's a miracle (but also EXTREMELY dumb on their part) they didn't just outright kill Ellie and Tommy right then and there, especially Tommy.