Rubio answered the questioner by saying he respected the guy's right to be a non-believer. The questioner seemed to have impression that Rubio, by telling of his base beliefs through a media ad, somehow interfered with those of his own.
Rubio would have done himself a favor had he stopped there. But he went on to reveal the real problem. If Rubio really believes what he claimed I don't see how we can trust him to protect our rights, or to protect the country in the face of mortal threat.
He claimed rights "come from God", and don't exist without one ("If there's no creator, then where do your rights come from?"). That's a misunderstanding of the concept of inalienable rights that hangs perilously on Rubio's faith. If he loses his faith he would, apparently, have no qualms in using government to violate our rights.
He also was very clear that his main priority is the afterlife. For those of us who don't believe in the Christian version of the afterlife, it means he'll be focused on a fantasy rather than giving his full attention to the duties of the Presidency.
That's how Rubio's believes, as he represented them, interfere with the values and well-being of anyone who doesn't share them.