Per this otherwise excellent Politico article, Republicans have not "abandoned" their party's post-9/11 push for tolerance. Many prominent conservative Republicans never accepted President Bush's statement that Islam is a religion of peace and that it is fundamentally compatible with American society. 

38 percent of Americans in 2006 said they would never vote for a Muslim for president, just about the number who said they would never vote for a gay person. In December of 2004, Cornell released a survey showing that half of Americans consciously told a pollster that they would favor a curtailment of civil rights for Muslims. About 40 percent of Republicans had explicitly anti-Muslim views in the survey.

What's fascinating -- and disturbing -- about prejudice against Muslims is that it is not driven by the same factors that have marginalized immigrants and minorities in the past. There are no economic incentives to push Muslims to the outside; there is an instinctive mistrust of Islam within evangelical Christianity and a very persistent post 9/11 ideological gulf between average and elite Americans. As of 2010, 43 percent of Americans admitted feeling bias against Muslims.