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The howto says:

UrlToolkit {
    ToolkitID = kohana
    Match ^/(application|system) DenyAccess
    RequestURI exists Return
    Match ^/(.*) Rewrite /index.php/$1
}

VirtualHost {
    ...
    TriggerOnCGIstatus = false
    EnablePathInfo = yes
    UseToolkit = kohana
}

Set $config['site_domain'] to '/' and $config['index_page'] to ''.

Well, a lot of these steps can be ironed out by using:

UrlToolkit {
    ToolkitID = kohana
    Match ^/(application|modules|system) DenyAccess
    RequestURI exists Return
    Match ^/(.*) Rewrite /index.php?kohana_uri=$1
}

Shorter as it doesn't require PATH_INFO. It also works with $config['site_domain'] = '/'. It includes 'modules' deny rule - also a part of the Kohana cascading file system.

Thanks!