The New York Times and the U.S. bishops appear to have very different understandings of President Trump's motivations, but do seem to arrive at an equally negative conclusion. First, here is Times' editor David Leonhardt's take, titled "Trump Flirts With Theocracy":
Let’s not mince words. President Trump’s recent actions are an attempt to move the United States away from being the religiously free country that the founders created — and toward becoming an aggressively Christian country hostile to other religions. ... On Friday afternoon, of course, Trump signed an executive order barring refugees and citizens of seven majority Muslim countries from entering the United States. It was his way of making good on a campaign promise to ban Muslims from the country.
The order also said it would eventually give priority to religious minorities from these countries. And if anyone doubted who that meant, Trump gave an interview Friday to the Christian Broadcasting Network, explaining that its goal was indeed to help Christians. Fortunately, many Christian leaders are opposing the policy.
I expect that Trump’s attempts to undermine the First Amendment will ultimately fail. But they’re not guaranteed to fail. He is the president, and he has tremendous power.
The attempts will fail only if Americans work to defeat the White House’s flirtations with theocracy — as so many people began to do this weekend. This passionate, creative opposition may help explain Trump’s weakening of the ban on Sunday. Yet the struggle to defend American values is clearly going to be a long and difficult one.
The USCCB has now released a joint statement, signed by Cardinal Daniel N. DiNardo of Galveston-Houston, president of the U.S. Conference of Catholic Bishops (USCCB), and Archbishop José H. Gomez of Los Angeles, vice president of the USCCB, which states in part:
The bond between Christians and Muslims is founded on the unbreakable strength of charity and justice. The Second Vatican Council in Nostra Aetate urged us to sincerely work toward a mutual understanding that would "promote together for the benefit of all mankind social justice and moral welfare, as well as peace and freedom." The Church will not waiver in her defense of our sisters and brothers of all faiths who suffer at the hands of merciless persecutors.
The refugees fleeing from ISIS and other extremists are sacrificing all they have in the name of peace and freedom. Often, they could be spared if only they surrendered to the violent vision of their tormentors. They stand firm in their faith. Many are families, no different from yours or mine, seeking safety and security for their children. Our nation should welcome them as allies in a common fight against evil. We must screen vigilantly for infiltrators who would do us harm, but we must always be equally vigilant in our welcome of friends.
The Lord Jesus fled the tyranny of Herod, was falsely accused and then deserted by his friends. He had nowhere to lay His head (Lk. 9:58). Welcoming the stranger and those in flight is not one option among many in the Christian life. It is the very form of Christianity itself. Our actions must remind people of Jesus. The actions of our government must remind people of basic humanity. Where our brothers and sisters suffer rejection and abandonment we will lift our voice on their behalf. We will welcome them and receive them. They are Jesus and the Church will not turn away from Him.
It's important to point out, I think, that neither of the above texts actually links to or quotes from the executive order in question (here is a link to it at CNN; the White House site is inaccessible as I write this). You will search the order in vain to find any direct reference to Muslims or Islam.