Is she talking about the coffee or something else?

Arael said:
Is she talking about the coffee or something else?

Could we put a Sexually_suggestive tag to it then?

I think it's referring to an episode in the manga where she accidentally burns her hand with hot water while trying to make tea for Shinji. Shinji shows her how to properly make tea and she remarks that although tea tastes bitter, it is warm (it has a nice warm feeling to it).