Science fiction and fantasy have always been metaphors on the human condition, though for some reason it took Joss Whedon
to make everyone remember this. PD is one of a large family of lovely shows that may fairly be called post-Whedon, in that they are much less interested in the nature of "magic" than in the effects it has on people, real people who don't feel chosen or special or even worthy, but who have no choice but to fold the bizarre into their daily lives as best they can.
PD is about a lot of things—self-image, forgiveness, acceptance, moral culpability, the impact of the past on the present—but mostly, I think, it's about how we relate to the people we love, and how they inspire us to grow and change. Even if it hurts, as change always does.
At the beginning of the series, Ned is living in sad, self-imposed isolation from the world. He has held himself apart for so long that he's never really formed an authentic self, and views himself mostly in terms of his strange gift. When Chuck asks him, in "Dummy", if he has any hobbies, we can see in Ned's half-horrified half-stunned expression that he does not, because all his mental energy is taken up with The Secret.
It takes Chuck to jump-start his life—just as, fittingly enough, her own metaphorical and literal lives were jump-started by Ned—and soon Ned is stumbling his way into relationships with the people around him instead of choosing loneliness. He makes genuine friendships, out of what had previously seemed to be purely business relationships, with Olive and Emerson. He finds parental figures, however eccentric and unwilling, in Chuck's aunts. He befriends Randy Mann. He learns to put aside twenty years of ugly feelings, and embrace his half-brothers. He struggles towards forgiving his father, knowing he must, and not for his father's sake, either. Little by little, Ned lets go of the pain he's been carrying; until, by the last episode, he has finally come to terms with who and what he is, and—with Chuck by his side—takes that last, breathtaking leap into the unknown... and willingly tells another person his secret.