htaccess files protect the directory and all subdirectories unless there is another htaccess file in the subdirectory, at which point that one takes over for its directory and its subdirectories.
an easy way to do this is to add in the domains you want hotlinkability from in your main htaccess file, ie, add in this type of line:
RewriteCond %{HTTP_REFERER} !^
http://www.otherdomain.com/.*$ [NC]
RewriteCond %{HTTP_REFERER} !^
http://otherdomain.com/.*$ [NC]
that will allow
www.otherdomain.com and otherdomain.com to hotlink but still stop everyone else.
cheers,
Luke