O'Reilly was talking over him and his other guests and kept repeating ad nauseum a run-on sentence about background checks, registration, and forbidding transporting certain firearms across state lines (he was for 'allowing' the states to determine what was and wasn't banned instead of the feds.) He then kept asking his guests repeatedly if they agreed with him. I think Rubio answered "yes" because he is for background checks and by doing so it sounded like he was agreeing with O'Reilly's whole platform. And I think he (Rubio) wanted to move the discussion along.
I think O'Reilly is straddling the issue but is more on the pro-2A side and needs educating (if his ego will allow it) on why registration and his bizarre interstate transportation idea are bad. I think in the end he could be a net positive on the debate.
Also, like other journalists O'Reilly keeps linking gun registration with car registration. We need to call these people on this that it is a totally irrelevant comparison. Driving a car is not protected under the Constitution and federal law already forbids creating a firearms registry for a good reason. Nobody in some future government is going to use a DMV database to confiscate your car.