There are two ways to do this.
you can add a robots meta tag to your index page
<meta name="robots" content="noindex,follow" />. This will instruct all web crawlers to follow the links on the page but not index the page itself.
You can create a kill_exact.cfg file that contains the URL of your homepage. Funnelback will then exclude this page from the index at index time.
Details on kill_exact.cfg can be found here:
To create the file you need to log in to the administration interface, switch to your collection then access the file manager (browse collection configuration files, from the administer tab)
Then you create a kill_exact.cfg using the create dropdown and add the URL of the page to kill to the file. You can apply the kill straight away by reindexing your site - run an advanced update / reindex the live view from the update tab in the administration interface.
It's also possible to kill entire sections using the kill_partial.cfg - this removes all pages starting with a common URL prefix from the index.