YOu *always* need the sub-folders.
Every mod distributed starts with a folder name that is typically the same as the name of the mod itself that contains a {mod_name}.toc file among other things... typically also a {mod_name}.lua and/or a {mod_name}.xml file.
For example... with nUI's latest development release you have the following...
Code:
nUI_5.03.02_Dev.zip > nUI -- nUI.toc
|----- bindings.xml
|----- Bars ------ nUI_Button.lua
|--------- nUI_ButtonBar.lua
(etc)
In this case, the "nUI" directory at the root of the ZIP file the one that you want to pick up and copy to the [ Interface > AddOns ] directory.
The same would be true of any other mod you download... it's always the directory at the very root of the ZIP file that you want to copy to the [ Interface > AddOns ] directory. If the mod is like Carbonite and has multiple directories at the root of the ZIP file, then you need to copy all of those directories to the [ Interface > AddOns ] directory.