git rebase -i presents an empty MacVim file
For atom I was able to fix by adding the wait flag to gitconfig (reference https://help.github.com/articles/associating-text-editors-with-git/)
[core] editor = atom --wait
I was using Macvim and needed to run mvim with the -f option, as documented here: GIT_EDITOR not working with macvim
You should not even have to look at the git-rebase-todo file. Vim should display a noop line and some comments. After saving that, you should get "Successfully rebased and updated ".
You are either using an old version of git, you have a broken git install or you have touched the .git folder in some way to cause it to behave this way.