A bare repository in git does not include a checkout. So in order to set the default branch that users will get after they clone, you cannot use git-checkout mybranch.

Instead, if you want the default branch to be something other than master, you need to do this:

git symbolic-ref HEAD refs/heads/mybranch

Which will update the HEAD file in your repository so that it contains:

ref: refs/heads/mybranch

This is well documented in the git-symbolic-ref manpage but it's not necessarily the first place you'd think of looking.