How is it not the same as calling someone fat?
Because, despite the fact that an individual person is intending to be rude (and I agree it's rude, as I've said), everything in our society suggests otherwise, that in fact a size six is ideal, rather than 'too thin'. The OP sees her body type on magazine covers and catwalks and playing the heroines in films, and getting a body the size of hers is the object of a multi-billion-pound diet industry which preaches body types such as hers as the ideal.
If she were being criticised by the same equally rude person for being too fat, she would have the entirety of our society from the media, the NHS, the diet and fashion industries etc etc backing up the rude person in agreeing that yes, her body is wrong and it's legitimate to criticise it or want to change it.
It doesn't alter the rudeness of the person making personal comments, but surely it's pretty obvious that there's a difference between pointing out thinness in a world that thinks that thin is good and pointing out fatness in a world where fat = unhealthy, undesirable, unself-controlled, disgusting etc etc etc even as we get fatter as a society.