Ohloh is a ... very web 2.0-y thing. Which means a lot of perl projects don't get registered, since we're not as whole an amazingly "woo! random social stuff! must register now!" community. I tried to redress the balance, discovered Ohloh's indexer had a bug that threw away half the history of my projects and thereby made them look much less actively developed, reported it twice, got ignored, and gave up.
Plus Perl5 generates a lot more search.cpan.org searches than google searches during normal use - we don't generally hit google very much because it doesn't have the information we need. So I could argue that CPAN's been getting better and Python and PHP have continued to fail at having an equivalent. And I'd be making just as much of an unfounded guess as both you and the article attuhor are by guessing web search volumes matter.
Of course, http://www.tiobe.com/index.php/content/paperinfo/tpci/index.... shows Perl5 and python and ruby all losing ground, but the other two significantly faster. I'm sure if I tried I could find you plenty more statistics that look good for Perl5 but don't really prove anything :)
If you do Google Trends searches for "perl programming", "ruby programming", "python programming", and "php programming"; you'll notice that they all show a downwards trend.
So I think there is something deeper here than "everyone is moving away from Perl".
Fact check:
http://www.google.com/trends?q=perl&ctab=0&geo=all&#...
Perl has been losing ground, while Python and PHP gain ground, for almost ten years:
http://www.ohloh.net/languages/compare?commit=Update&l0=...