This article at The Atlantic reveals part of what was wrong with the Court's ruling on the Muslim Ban and how the ruling gives the administration a green light to discriminate. The author demonstrates how for Justice Roberts the only discrimination that is illegal is when it is explicitly stated, discriminatory effects alone don't count. By this logic of Roberts's, most of the Jim Crow laws banned by the 1965 Voting Rights Act would be okay.
Also, the strange inconsistency (hypocrisy) of the last month:
1) Vaguely "anti-religious" statements of a minor public official in Colorado mean the baker didn't receive due process and his religious freedom was denied, yet
2) Explicitly Islamophobic statements by the President are not relevant, so no one's religious freedom was discriminated against.