Hi Gavin,
You could also create a user account in Matrix for Funnelback to crawl the Matrix site as.
You would need to ensure this user had read access to all of the pages you wanted to index, and then configure the Funnelback web crawler to perform an authenticated crawl of the site (logging in as a user then crawling). Keep in mind that this would result in Funnelback crawling the site as though it was logged in to Matrix (so this could result in Funnelback seeing some unpublished content if the Funnelback user has access to it)
regards,
Peter