find . -mindepth 1 -type d -exec echo cp index.php {} \;
The above command would copy the index.php file from your current directory to all subdirectories, recursively – but not right away.
When you've made sure it prints all the correct copy commands, remove the echo and execute it. echo is just a safeguard to show you what the whole command would do before actually doing something you might not want.
Another interesting approach – thanks @RedGrittyBrick – would be to symlink the files instead of just plain copying them. This way, the index.php files in the subdirectories would all just be a shortcut, so to say, to the one in the root directory and not duplicated. To do this, in the above command, change cp to ln -s. This way, when you change the "master" index.php file, all the others in the subdirectories would still point to it and thus automatically change as well when viewed.
For completeness, the whole command, broken down, works like this:
find ., search in the current directory-mindepth 1, going at least one directory deep-type d, only find directories-exec …, execute the command echo cp index.php {}, where {} is replaced with every directory found. This command is called multiple times, once for each subdirectory.
