The reason I believe many consider it a Muslim ban is that Christians have a slyly worded exemption/preference.
http://www.npr.org/sections/thetwo-way/2017/01/29/512272524/of-courts-and-confusion-heres-the-reaction-to-trumps-immigration-freeze
It should be noted that the executive order signed Friday tells officials to "prioritize" people suffering from religious-based persecution — provided that those people are members of a "minority religion" in the majority-Muslim countries covered under the ban. In many of those countries, Christianity is the main minority religion.
Seems Cristian groups oppose this preference. http://www.politico.com/story/2017/01/trump-immigration-christians-234341
EDIT(Based on further research): Although portrayed in the media as a christian exemption the text found in the below link does not specify any particular religion, only that they are a minority religion. http://www.npr.org/2017/01/31/512439121/trumps-executive-order-on-immigration-annotated