Right, but Rails will always have some sort of organization. That being said it is possible to go against the grain and not use Rails' default directory structure - but that's difficult.
I'm comparing Rails to vanilla PHP - just as the author is. People are exposed to PHP's low barrier of entry (again, vanilla here) because you can write an application with PHP/Apache/mySQL very quickly. However, because of this, most instances are very hacky.
You don't think Ruby on Rails requires the overhead of a server???
There are perfectly good and very sophisticated MVC frameworks available for PHP, such as CakePHP (one of the closer to Rails, even down to the command-line "baking" of models, controllers, etc.).
There are meaningful differences to development using both languages, but criticizing PHP because it was popularized independently of any specific framework is not one of them. Especially since there are plenty of situations (think dumb but scalable web services) in which the last thing you want to do is invoke the overhead of a framework in any language.
I'm comparing Rails to vanilla PHP - just as the author is. People are exposed to PHP's low barrier of entry (again, vanilla here) because you can write an application with PHP/Apache/mySQL very quickly. However, because of this, most instances are very hacky.