As have been pointed before, the CIO article isn't really about Perl usage, and the counter examples aren't very interesting either. The writer warns against using Perl in:

• Real-time or high-performance applications - This doesn't have to do with Perl specifically, however, if said real-time app needs a text-oriented language, embedding Perl in the code can bring some benefits; ignoring this makes this item more of a half-baked populistic advice, and mostly a buzzword-ish one.
• As a replacement for shell scripts - Actually a good advice, using Perl as solely a one-liner language where simpler options are available is a good practice, as well as not relying on system calls and back-ticks.
• As a Web scripting language, which is another buzzwordish-compatible concept, albeit a bit off, especially since "more modern Web scripting languages", aren't.
• And, In an obfuscated fashion - Is a "best practice" item, nothing to do with Perl, as obfuscated code existed before Perl existed. Overall, along with item 2, this isn't a "don't use Perl", but more of a "use Perl, but don't do this and that".

But the main issue is, the writer doesn't really gives any advice as to when to use Perl, and what are the preferred usage of it other than "Perl has these features, it's not C, I prefer rails, and don't write bad code".