Are you suggesting that it is bad that PHP applications often have a request path that relates to the folder structure?
In other words, are you suggesting that simplicity means an application should not have a request path that relates to the folder structure?
To give an example, are you saying it's a bad thing that example.com/profile/ loads /profile/index.php, rather than passing /profile through a single controller function to identify what code should be responsible for handling it?
The first approach actually seems pretty straightforward paradigm and it's what most new programmers would expect. Adopting a MVC/routes method is more complex and arguably overkill for a simple application.
If that is what you are contending, it should be said that PHP does not require this approach. Although it is often a preferred approach, because it doesn't depend on additional web server configuration.