What made "You'd better!" a threat?

"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."