Danny likes Holly well enough on her own, but he questions her relationship choices. Like, a lot. He can't believe someone so sweet and otherwise reasonable would be friends with such an unbelievable douchebag. He really, really wants to just guide her away and tell her, "no, honey, you can do so much better."

But he learned his lesson from that one confrontation, interfering is not going to help anyone. He'd be a lot more protective of her, if being protective didn't lead to threats of murder. So he's backing off and not doing anything overt about it, but he is keeping a general eye towards her, just in case. He's just worried--even if she can take care of herself. Anyone who has seriously attempted murder is not somebody to hang out with. (Seriously, Holly. Get your relationship decisions sorted out.)

But yeah uh most of his interaction with Holly has been through Skyler, basically, although they're starting to branch out a little now. So most of his opinion on her has to do with his opinion on Skyler too, HAHA