I know you are looking for a regex solution, but just in case you change your mind, maybe something like this would suit your needs...

Updated: to handle parentheses.

#!/usr/bin/env perl

use warnings;
use strict;

while (<DATA>) {
    #my @no_reds = grep { !/^r/i } split;
    my @no_reds = grep { !/^r/i } split /[\s\(\)]/; 
    print "@no_reds\n";
}

__DATA__
 12345 Gray 6789 Red 
rd 555 blue 888 red 777 green 999
foo bar r baz ruby
goo(r)  ruby doobie
888red999
[download]

Prints out:

12345 Gray 6789
555 blue 888 777 green 999
foo bar baz
goo   doobie
888red999
[download]

Unlike ikegami's solution, this requires the input to be whitespace-separated.