[Merlin Cori]

тогда так....
убираем строку со split

#!/usr/bin/perl -w
$input_file="rus_networks_secret_file.txt";
$out_file=".htaccess";
$text="Allow from ";
open(HANDLE_IN, $input_file) or die ("Error open file", $input_file);
open(HANDLE_OUT, "> $out_file") or die ("Error open file");

print HANDLE_OUT "Options -Indexes\nOrder Deny, Allow\nDeny from all\n";

while(!eof(HANDLE_IN) )
{
$input=readline(HANDLE_IN);
$output= $text.$input;
print HANDLE_OUT $output,"\n";
}