That's because python and ruby sites do the right thing: a page is not a script, the url should not point to a "file" ("index.php" and such). When using python or ruby, most of the time you use frameworks that let you define your urls, and not just put a script and let the url point to it. Urls should be readable and easy to remember, they are directions for the user. Wich script is running on the server is an implementation detail that shouldn't be part of the user interaction, he doesn't need to tell you wich script to run.

"mysite.com/add_user" is waaaaay better than "mysite.com/add_user.php"

This is one of many bad things php encourages you to do... and that's why most good programmers don't like php, because it makes easy to do bad things.

Some big sites using python: youtube.com, addons.mozilla.org, dropbox.com, disqus.com, ...

Big sites using ruby: twitter.com, jango.com, ...