does .htaccess protect subfolders?
 

If I make a .htaccess file for antihotlinking and put it in my root, will it protect all the stuff in the subfolders too?

It will, and on the other hand if you put it in a subfolder, directories above it won't be affected.

Just so you know, if you don't want it to affect subdirs then just drop another .htaccess file into the subdir and for any file inside that subdir or deepr it will override any .htaccess below it.