When and why did the expression "You'd better!" come to have threatening undertones? The structure seems to be helpful in its essence (e.g., "You had better throw out that banana or fruit flies will start to gather.") but its shortened version always feels like it's lacking an unsaid "...or else!"
"You'd better" is only a threat in specific contexts, or when said in a threatening tone of voice.
Consider this typical conversation:
Allan: Hey Betty, I'm not sure which option to choose. This first one is faster, but the second one is cheaper. I don't have a lot of time to lose. Should I choose the faster one?
Betty: Yeah, you'd better.
This is not a threat at all, and not even a warning; it's really a confirmation of Allan's idea. There is certainly something left unsaid, but it's not "or else I'll come after you," it's simply, "or else you might not make it in time."