What evidence do you have that people of minority religions are being persecuted any more than people of the majority religions? In a country like Syria that is ~90% Muslim, what are the odds that all of the most persecuted people are in the 10% religious minority?

Why even flag them based on religion anyways if you are trying to help people who are being persecuted or murdered? What difference does it make?

During WW2, nobody should have been saying yes or no to Jews solely because they were Jews. It was because the were as a people being persecuted and murdered solely because of their religion that they should have been helped.

And again context is important here. The ban is coming from a person who has stated Muslims should be banned from entering the US because "there is great hatred towards Americans by large segments of the Muslim population" and "it is obvious to anybody the hatred [of Americans by Muslims] is beyond comprehension". To ascribe motives to the ban that are counter to what the author of the ban has said again and again seems very dubious.