The last time someone said "I feel your pain" to me was when I biffed my car on a wall after slipping on ice on a steep hill. I understood that to mean that the person understood the annoyance about the buggeration of damaging my car, the metaphorical pain. Actually the car in question, still dented, is still going strong. It recently told us its name is Slumdog so I don't think it minds a dent or two. Just as well really.
Anyway, that is what I was thinking of when I said that I think the expression is used, more often than not in my opinion, as a figure of speech to express sympathy. Perhaps it was my including the word 'just' that caused the problem. Semantics does matter, after all. In which case I hereby withdraw the word just and apologise for its inclusion. In the heat of the moment and all that....