Faith-based groups minister to all individuals regardless of who they are. That's the point of faith-based ministry--to reach out in redemptive love and service to everyone.
Hiring individuals who share this faith commitment helps insure consistency with the core faith-based values of love, justice and compassion that motivate faith-based ministry. Both the Obama and Bush administrations have considered that approach reasonable, and faith-based groups maintain that it's essential.
Assuring that employees actually believe in an organization's core values is also just plain common sense. Imagine the insanity of forcing a Jewish group to hire a Muslim who denies the Holocaust, or forcing a Muslim group to hire an atheist who burns the Koran, or forcing a Christian group to hire an agnostic who considers the ministry, death and resurrection of Christ a hoax.
Some agents of intolerance wield the non-Constitutional phrase "separation of church and state" as if it's a government billy club. Yet rather than banning faith from the public square, the First Amendment actually protects it, providing that "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof…." U.S. government policy on religious hiring rightly reflects this freedom.