Most of the time desktop apps and web apps serve completely different purposes. Desktop apps do not intend to be flashy or beautiful, they need to be usable for getting things done. They should follow the conventions of the OS, be fast and intuitive. So when a GUI developer creates a GUI that is highly usable and not showing off with eye candy, the GUI developer has done his job properly. Saying "they get away with it" because desktop GUIs are ugly is just wrong.
Web sites often need to draw attentation. They want to sell something, be interesting. They should be flashy and beautiful.