Are you referring to running the file on your server, or opening the file to edit it? Maybe I'm the one who misunderstood, but it sounds like Kiwiberry read you wrong.
.pl files, as Kiwi said, are PERL scripts, and require PERL installed on your server to open and function currently. If you've put the file on your server and are trying to run it from your browser, and are expecting to see a login/password dialog but aren't getting it, then chances are that either your server doesn't have PERL installed, the file is located in a directory not recognized as a scripts directory (ie. cgi-bin), or there's something else wrong with the way your server handles PERL scripts.
Hope this helps you out. Of course, perhaps Kiwi already answered your question, but I've never heard of a password protected plain text file, so I just thought I'd offer an alternative answer.