Options +FollowSymLinks
RewriteEngine on
RewriteCond %{REQUEST_URI} !/index\.php$ 
RewriteCond %{HTTPS} !=on
RewriteCond %{HTTP_HOST} !^subdomain\.site\.com
RewriteRule .* https://%{HTTP_HOST}:443%{REQUEST_URI} [QSA,R=permanent,L]
RewriteCond %{HTTP_HOST} !^www\.site\.com
RewriteCond %{HTTP_HOST} !^subdomain\.site\.com
RewriteRule (.*) https://www.site.com/$1 [R=301,L]