I've heard variations on this story for the last few days and I wish I were surprised it keeps getting reported with all of the relevant portions removed that make it a non story. If you listen to the raw audio or read the text you will see he basically ignores the question that was asked and talks about building a wall to control illegal immigration.
Reporter : "Should there be a database system that tracks the Muslims that are in this country?"
Trump : "There should be a lot of systems, beyond databases. We should have a lot of systems, and today you can do it. But right now we have to have a border. We have to have strength, we have to have a wall, and we cannot let what's happening to this country happen again."
REPORTER: But is it something your White House would like to implement?
TRUMP: Oh, I would certainly implement that, absolutely.
REPORTER: What do you think the effect of that would be? How would that work?
TRUMP: It would stop people from coming in illegally. We have to stop people from coming into our country illegally.
If you only react what someone tells you is true and don't check the raw information it's easy to be misled. Trump will say a lot that some people won't agree with or downright hate, but at least let it be his stances you don't like and not a reporter inferring what he meant by interpreting the answers to fit the scenario he prayed would play out or a channel editing it to make the soundbites fit the emotion they want to place in you.