You get this error if `~/.emacs.d` exists but is not a directory readable by your user. From the partial output of `ls -la ~/.emacs.d` you gave, it appears that you somehow managed to get a `.emacs.d` directory in your user's home directory that's owned by root and has no permission for your user.
You could try (as root)
chown -R user:yourgroup /home/user/.emacs.d
where `user` is your username and `yourgroup` is your user's primary group.