Native U.S. English speaker here.
People say, "I am not that bothered BY IT/SOMETHING," because something has to not be bothering you. People might be more likely to say, "It doesn't bother me". It means:
I'm not upset.
I don't care about it.
It has no effect on me.
I have never heard anyone say "I am not that bothered" in the context of talking about what restaurant to go to. Maybe it's a British thing? I don't know, but no one says that here in that context. People say, "I don't care," or "it is all the same to me" when talking about where to eat, but not "I am not that bothered."