Fixing The WordPress.com Custom CSS Plugin 

That plugin is custom to WordPress.com, so it’s not really for wide usage yet. But I did find these notes for WPMU usage:

I needed to do two things to make it work:

On line 131 change is_int() to is_numeric():

if ( is_numeric( $blog_id ) ) {
switch_to_blog( $blog_id );
$current_plugins = apply_filters( ‘active_plugins’, get_option( ‘active_plugins’ ) );
}

Then in my .htaccess add the following:

RewriteRule ^custom-css.php /index.php [L,QSA]

Now works a treat.