I think what made Clark listen was because of three things. One, as Ann pointed out, he is Clark's dad, and the male authority. Two, he is male, and therefore relates to Clark's side more than Lois'. But three, because Jonathan agreed with Lois' threat to print it, even though he was the strongest advocate of protecting the secret, arguing against telling Lois at the beginning (not of this story, of the series.) Clark would expect his mom to agree with Lois, being a female and not being so vocal about protecting the secret. But his dad is the one he'd least expect to say those things, and to criticize him so openly. Martha voices her disapproval with some of Clark's decisions quite often, but Jonathan is usually more laid back in relationship matters, so it probably took him more by surprise.
