With PuTTy you have to open a separate application and configure connection in a completely different manner. Compared to Linux/OSX which enables a "work in a terminal" model, where "ssh", "scp", etc. are commands that can be used from within an existing terminal. It feels like a completely separate tool from the terminal instead of integrated with the terminal. I think this is a similar argument that users of text-based-editors (vim, emacs) have over using GUI-based editors.