I think I can explain that. A real GUI provides more than just visualization, otherwise you'll have to re-invent the wheel and will likely miss important platform conventions. You need support for drag & drop from and to outside the application, standard folders and standard file/folder Open and Save dialogs, command/action abstractions to implement unlimited Undo/Redo, near arbitrary keyboard shortcuts for all menu entries (which adapt to the platform conventions somehow), standard Quit, Print, Page Setup and Help menus, support for internationalization, support for platform-specific layout guidelines (spacing, default buttons, button ordering), tray icon support, support for platform-specific notification and indexing APIs, programmer access to file icons (surprisingly tricky on Linux), standard packaging and deployment, support for code signing, and so on and so forth.

Most "browser-based" applications don't even get basic keyboard shortcuts right. Only few of them are really usable and not a single one has better functionality then its native counterparts. There is a bit of a bubble around web "apps" created by a startup culture. The problem is that most of those startups die within a few years. I'm not saying that a browser-based app cannot be useful, but it's equally important to be aware that many types of applications require a real GUI. It doesn't have to be native (e.g. Qt is not "native" in the traditional sense), but it needs to be fairly complete and respect platform APIs.