Do you mean "hidden", i.e. invisible folders, or "Packages", such as applications, which are in fact folders containing many files inside? It sounds like you're talking about packages.
A folder is a package when a specific bit is set in the folder's meta-data on the disk. Usually, things need to be packages for them to work properly.
AFAIK, there is no setting for the Finder to treat packages as folders. The Terminal treats them as normal folders, though.
Do you find yourself going into packages a lot....?