The United Church of Christ, the National Association of Evangelicals, the U.S. Conference of Catholic Bishops, the Lutheran Immigration and Refugee Service, the Unitarian Universalist Association, the Religious Action Center for Reform Judaism, the Episcopal Church have all raised objections to Trump's ban on Muslims (let's be honest about that). Some of those churches, as well as the Evangelical Lutheran Church in America, the United Methodist Church's Council of Bishops, the Union for Reform Judaism, signed a letter against Trump's ban. The Southern Baptist Convention sent a letter this morning protesting the ban.
That list doesn't include Muslim groups, and secular groups, and individuals like Fr. James Martin, also listed at the links, who protested Trump's action.
Interestingly, the objections of all those groups, except for the SBC, were made last week, before Trump signed the order on Friday that created so much controversy and chaos over the weekend. It was announced; the news was available. Religion News Service and Huffington Post reported on it as late as Friday, as early as Wednesday, and yet on the news channels over the weekend: