mod-rewrite to ignore the subdomain

Question

I'm using a mod-rewrite for pretty URLs, meant to run on the domain root. Working fine but now I'm trying to make it run on a subdomain and it keeps giving "500 Internal Server Error".

The subdomain automatically redirects to the folder with that name on my hosting account (sub.domain.com shows the content of domain.com/sub/). Does it fail because this request is already being mod-rewritten automatically or can I simply change something in the htaccess to address the subdomain instead?

Options +FollowSymLinks
IndexIgnore */*
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . index.php