"Compared to the alternatives the author suggests? Ruby and Python combined are doing less than Perl. PHP is the runaway favorite [w3techs.com], but if you dig into the numbers, you'll find that most of the change is due to Content Management Systems which by and far have been developed on PHP. So these massive zomfg numbers PHP is pulling in isn't due to people programming with it as much as they are copy-pasting it en masse."
Yes, because somehow all of those PHP sites are running 'copy-pasted' code and all those Perl sites are running custom code ... you're clawing at straws here. These sites are using PHP because obviously it's the better choice. It's just as easy to 'copy-paste' a Perl CMS as a PHP CMS. However, nobody's doing that, judging by the numbers.
And then again: 'copy-pasting' as you call it is a perfectly legitimate reuse of code. I'd rather call it installing a tried-and-proven system. Ever heard of DRY and not trying to reinvent the wheel?
Regarding the unnoticed custom back-end stuff: PHP does fine on CLI. I've loads of PHP scripts running as cronjobs. BASH scripts as well. No Perl. Why not? Not because I can't program Perl, it's because the syntax is so head-splittingly different from the whole C family AND (here it comes) Perl has _absolutely_ no advantage over either PHP/CLI for database batch jobs and such or BASH for shell scripting. It might be faster than PHP, but on batch jobs involving large datasets your database is always going to be the bottleneck, so who cares?
Perl has been at a standstill compared to PHP and other scripting languages. I know PHP is not very popular here on slashdot but it has made some pretty serious advances in the last few years. Decent frameworks like Zend, Symfony and Laravel have made develop very much quicker. Stuff like Doctrine and Propel ORM's have given PHP access to some pretty powerfull data modelling and storing/retrieving methods. Integration of Solr and Varnish have given it very fast searching and caching solutions. And finally, whilst PHP consistency in syntax still sucks (stuff like function arguments and naming are terrible) improvements to the OO capabilities in PHP5 have taken away a lot of the rough edges it once had.