It also has the advantage that if you extract the zip you can now access whatever pieces are inside as separate files even by tools that don't understand the containing format. (eg a bunch of jpg/png inside the zip are perfectly viewable in any image viewer). Trying to do the same with SQLite is problematic as you have to write queries to grab the blobs and then dump them to disk.
Where SQLite as a format does shine is if you need to keep historical information such as an undo/redo log. That makes it good for an application format, but not for an interchange format.