Subfolders with PHP

No, definitely not. When you start building larger applications that need to scale you'll find that mapping urls/pages directly to files won't serve you well. This is due to the large amount of code you'll be having to repeat in each of your index.php files. You should look at implementing a front controller pattern: http://www.sitepoint.com/front-controller-pattern-1/

In a nutshell, you're basically routing every request to your site/app through the index.php file. Once the request reaches that file, you can examine the url to determine which files you need to include (via include, require_once, etc) to execute the given request. This pattern is used by every major php framework today (Laravel, Symfony, Cakephp, etc) and is very powerful. As an example of the benefits this approach provides, consider a full blown site with a rich layout (header, footer, sidebar, etc). If you implement a front controller pattern you can break your template into a separate file (or files) and include those inside the index.php file for every request. This would allow you to make changes to your template and it take effect for every page in your site. If you don't use this pattern you're pretty much going to be repeating the same HTML across every .php file in your app. This violates the DRY (don't repeat yourself) principle. Making even the smallest change to your template (e.g changing the copyright year) would have to be repeated for every file in your app. If your app is large you might find yourself changing hundreds of files. Hope this helps!