qr// is a regular expression quote, and as such does, in a sense, compile regular expressions. Unfortunately, you're using the regular expression as a hash key, at which point it's turned back into a string. As you process the Apache log file, $rule is just a string. When you use it as a regular expression, it has to be compiled again - each time through the loop.

If I were writing your code, I would store the regular expression rules/filehandles in an array. Here's a sketch of what it might look like:

my @rules; # not %rules.
...
# Process input file of processing rules
while(<INFILE>) {
   ...
   push @rules, {
      regex       => qr/$string/,
      file_handle => $fh
   };
}

...

# Read Apache log file and print to various other files
while (my $line = <STDIN>) {
   for my $rule_ref (@rules){
      my $regex = $rule_ref->{regex};
      my $fh    = $rule_ref->{file_handle};

      if ($line =~ $regex) {
         print $fh $line;
      }
   }
}
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Hope this helps.

WOW, never knew that. Thanks a lot the execution time went done to 22seconds.