The phrase often implies an apology or acknowledgement of inconvenience caused by the delay. I'm sorry to keep you waiting so long, the meeting ran over.
Pro Tip 2/3
Tone Sensitivity
Can imply frustration or annoyance if said by the person waiting, depending on tone and context. I've been kept waiting for over an hour!
Pro Tip 3/3
Urgency Indicator
Sometimes used to convey urgency or importance when someone's time is considered valuable. We can't keep the CEO waiting; let's hurry up.