Removing index.php causes Not Found error on secondary pages
Thanks to @brad-bell - his comment on another post pointed me in the right direction. I thought that I already checked on mode_rewrite but I didn't.


  The Apache mod_rewrite module wasn't installed, so the  block of Craft's default .htaccess file was being
  skipped not allowing index.php to be rewritten in the URL.


Enabling mod_rewrite solved the issue.