Where exactly is the mod folder in question, and what distribution method are you using for the game?
while the zip download of the game from factorio.com will use the mod folder inside the factorio game folder, other versions such as steam will instead use %APPDATA%\Factorio as it's user data directory, so %APPDATA%\Factorio\Mods is where you need to put the mod files.
if you don't know which you should be using, there is a file called config-path.cfg in the game's folder, it's just a text file, open it in notepad or something.
this lists a directory where config.ini can be found.
if it lists: config-path=__PATH__system-write-data_ _/config, then you need to go into %appdata%\Factorio and install your mods there.
I hope this information helps.