This phrase suggests someone's emotions were negatively stirred, often unexpectedly. The new policies didn't sit well with employees and certainly ruffled a few feathers.
Pro Tip 2/3
Metaphorical Imagery
Imagine a bird's feathers being disturbed - it’s used metaphorically for human reactions. He always speaks his mind, even if it means he ruffles someone's feathers.
Pro Tip 3/3
Not Always Intended
The phrase can be used when offense is given unintentionally. I didn't mean to ruffle any feathers with my comments about the event.