Greetings,
Another way to look at this problem is to use grep to simply see if $user[0] is in your @protected list.

open (PROTECTED, "$protected");
@protected = <PROTECTED>;
close(PROTECTED);

#... not sure where $tag is coming from...
if (grep($_ eq $user[0], @protected)){
    sock("PRIVMSG $tag:$user[0] Is A Protected User!");
}
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However if you are looking for a counter of where in the list $user[0] appears you can add one to your for loop.

my $count = 0;
for(@protected){
   if($_ eq $user[0]){
     sock(...blah blah blah...);
     last;
   }
   $count++;
}

print("$user[0] was found at ".$count+1." in the list.\n");
[download]

-InjunJoel