Because if the government wants, it can send you (US citizen or not) to gitmo, declare him as "enemy combatant," and poof, no Habeas Corpus for you.
So to argue that you may still use Habeas Corpus to challenge the government today is splitting hair - only if the government has chosen not to label you as an "enemy combatant."
In other words, whether or not you can use Habeas Corpus is not up to you (or anyone else) any more. It's up to the government. That, my friend, is not Habeas Corpus.