The idiom ‘my way or the highway’ forcefully expresses the view that ‘you can take it or leave it’. In fact, it really means ‘take it or leave’, as the highway refers to the road the listener should go down if they don’t agree with the speaker.
What is implied when the term is used by the boss in a work situation is that the employees are expected to agree to some proposal or ‘hit the highway’. That is, no discussion is necessary or allowed – do it the boss’s way or be fired.