- Nope, in PHP you don't generally put code in the web root.

- PHP and generally all the frameworks based on PHP are strongly encouraging putting code outside of the web root. Just take a look at directory structures in Zend Framework (http://framework.zend.com/manual/en/learning.quickstart.crea...) or Symfony2 (http://symfony.com/doc/2.0/book/page_creation.html#the-direc...)

- ...and almost everyone that uses PHP professionaly does that.