6 out of 7 countries on the ban list are active war zones. Which means they have unstable governments, poor infrastructure, and consequently poor documentation of their citizens, undermining any vetting process that might be employed during their immigration to the US.
For the most part, we have no idea who the people coming over from these countries are. Sure, most may be good people fleeing a conflict, but until there is a reliable way to evaluate the background of these individuals, it's anyone's guess.
That's what this ban is about. Temporarily limiting immigration from countries where it is difficult to assess citizens prior to granting them legal entry to the US, until measures have been implemented to do this.
It has nothing to do with "Muslims". Out of the 10 countries with the highest Muslim populations in the world, only one is on this list.