I've this RewriteRule that actually works too well :-)

RewriteRule ^([^/]*)/$ /script.html?id=$1 [L]

Unhealthy factor relating to this rule is it also matches physical sites which I'm not going.

How do i tell the mod_rewrite to disregard physical sites and apply the above mentioned rule only if your directory matched up doesn't exist?

Have a look at RewriteCond. Place the following before your rule to exempt out sites and files

RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^([^/]*)/$ /script.html?id=$1 [L]