That gives me a similar error except instead of trying to write to /var/www it wants to write to /root

Not sure, but maybe it would help to explicitly specify the place where you want the known hosts info to be kept, e.g.

my $ssh = Net::SSH::Perl->new(
        $remote_host,
        protocol=>2,
        options => [ "UserKnownHostsFile /some/path/.ssh/known_hosts" 
+]
                     # or "GlobalKnownHostsFile /some/path/.ssh/known_
+hosts"
    ) or die("could not connect");
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