sure, if you're writing "Hello world", /index.php is great. For everything else? Not so much.
This reminds me of people saying "version control, that's too hard, I'll just make backups of the src dir regularly".
If it's just a small brochure site with a few pages then it's no problem, but forums and larger projects built like this can leak information and expose vulnerabilities when PHP files which weren't meant to be directly accessed are, such as pages that perform SQL queries expecting variables in context that don't exist when accessed directly, or old config files, text files, open directories, etc.
But "url=page" is still basically routing using the query string, and IMHO so is access control using .htaccess. Any system where URLs are validated and where they don't directly point to files on the server counts.
Having a router may make it easier, but it's not the only way.
You can just put your libraries, passwords, etc., in some directory outside the document root.
/var/www/example.com/public
/var/www/example.com/lib
If you can keep it under control, though, of course it's no different than includes in C/C++ (it probably literally is a wrapper around the macros.) But modern PHP prefers using autoloaders, so you never actually have to use include statements to begin with. You could just as well define those directories and include them through a Composer setting.
Yeah, that's a pain. You have to exercise a little discipline. Of course none of my code has that ;)
With hand-typed routing, can't you accidentally define two routes that overlap, so some URLs could match both? The only reason it goes to one and not the other is something random like the order the routes are defined in the file? Like if you defined this route:
/a/b/c
/a/*/c
You can't do that with a filesystem, put two files in the same place.
To be fair, that's not random, that's pretty explicit. And if you're optimizing for speed, short circuiting at the first match is a good idea.
But if you're using a router, chances are you're passing the segments as arguments to some function or method anyway, so route /a/*/c and /a/b/c should both wind up returning the same content if the second segment in both cases is 'b'.
cough wp-config.php cough
I think while it is easier to use files as routing first time you use php.. once you start learn how to program, simple router is much much easier to reason about. Simple router is not the problem when learning php. Problem is clunky language with lot of legacy stuff and that people start with something like laravel that has so much stuff in it that you have to learn 20 concepts at once.