The phrase often implies a disdainful or unsympathetic attitude towards someone's plight. After losing his job, his colleagues put the boot in by mocking his misfortune.
Pro Tip 2/3
Metaphorical Hurt
It's not about physical harm but causing emotional or reputational damage. They really put the boot in by spreading rumors about her.
Pro Tip 3/3
Emotional Impact
Using the phrase can express disapproval of the harshness being displayed. It's unfair how the critics put the boot in when she was already struggling.