shrug So much of it comes back to how PHP was designed to be as low-barrier-to-entry as possible, for good and bad, and it's paying for its mistakes, and has done over and over and over.
I like how, for example, the article's author complains about the use as CGI except that on shared hosting (where most PHP really happens), there are limits to what you can do about that, and on any real system you'll be stacking it behind nginx with PHP-FPM anyway (which is a built in feature to run a pool of interpreters)
Then there's the point about how the whole PHP 'accelerators' market existed. Sure, it did. Still does if you want to handle encrypted scripts, too. Zend Guard and ionCube being the typical examples. But guess what? Precompiling scripts and running the compiled version is a core feature now.
Then we have the claim about how there's only one php.ini file. Again, that's not entirely the case and other options are available, especially important on shared hosting which is where PHP's real market is and pretty much always will be.
Then it talks about using insulating apps from each other and with different versions of PHP? HostGator et al don't seem to have a problem with any of this...
So yes, PHP has a lot of flaws. But so many of them are because of poor developer practice. And when you can get cheap hosting for any arbitrary Python or Ruby app, in the couple of dollars a month bracket, lemme know.