This phrase does have two meanings in US English, as agreed by other posters.
For the sake of completeness, I feel compelled to add that in British English, this is a phrase that would only be used when offering coffee. Using it as a question to affirm how much someone was enjoying their coffee would probably be understood, but would sound extremely odd. Instead, British people might say:
"Are you enjoying your coffee?"
"Is that coffee OK for you?"
Or something similar.
Divided by a common language and all that.