I think you're spot on when you say that people don't mean to be rude. In their mind they're trying to be funny. I also get the "your stutter is cute" bit. I often don't know how to think about that idea, so I have a rote response that's a little bit coy and deflects the attention (aww, you'll make me blush ... something like that). I wonder how many others get that as well. (and what their reactions are to it).