Right, I've done a small test.
To get what you want, you need to following:
- htaccess.txt (you don't need a .htaccess file)
- Search Engine Friendly URLs set to On
- Use URL rewriting set to Off
- You finally need to ensure that your Homepage menu items it set to a specific component such as an article or something else, not an Alias
This will ensure that you get example.com/index.php/home
Hope this helps