He told the Washington Examiner:
Johnson:Look. Here's the issue. You've narrowly defined this. But if we allow for discrimination — if we pass a law that allows for discrimination on the basis of religion — literally, we're gonna open up a can of worms when it come stop discrimination of all forms, starting with Muslims … who knows. You're narrowly looking at a situation where if you broaden that, I just tell you — on the basis of religious freedom, being able to discriminate — something that is currently not allowed — discrimination will exist in places we never dreamed of...
Examminer:You think it's the federal government's job to prevent—
Johnson: Discrimination. Yes.
Examminer: In all cases?
Johnson:Yes, yes, in all cases. Yes.
Of course, the libertarian position is that you should be free to discriminate against anyone for any reason if you so choose.
Johnson is about as libertarian as Al Sharpton.
For more on discrimination see: About My Racist Friends, My Homophobic Friends and My Own Prejudices.