The wicked flee when no one pursues (Proverbs 28:1)
Matthew Henry gives this commentary:
What continual frights those are subject to that go on in wicked ways. Guilt in the conscience makes men a terror to themselves, so that they are ready to flee when nonepursues; like one that absconds for debt, who thinks every one he meets a bailiff. Though they pretend to be easy, there are secret fears which haunt them wherever they go, so that they fear where no present or imminent danger is, Ps. 53:5 . Those that have made God their enemy, and know it, cannot but see the whole creation at war with them, and therefore can have no true enjoyment of themselves, no confidence, no courage, but a fearful looking for of judgment.
R. C. Sproul, in his book The Holiness of God, has a different take. He views it as a repulsion when unbelievers encounter the holy, even the tiniest holiness of God reflected in 1-part-in-109 homeopathic (my word, not his) quantities among believers. He relates an anecdote of a professional golfer who was part of a foursome with Billy Graham. After the round the pro returned to the clubhouse in a foul mood complaining to a friend that he didn't appreciate Billy Graham shoving his religion down his throat. But upon further questioning, it turned out the Graham had not mentioned his religion, not even once.
From my recollection as an unbeliever, I think Sproul is closer than Henry. When I was an atheist, the slight uneasiness I felt around believers (that is, around those who were not proselytizing. Around that type there was a profound uneasiness) was not that of a criminal fearing that an arrest warrant was about to be produced. It was a slight revulsion telling me that I should not stand too close to this person. He has cooties.
At any rate Henry and Sproul (and I) agree that the irony here is that there is, in fact, no persuit.
Sproul also discusses how people fear God much more after they come to know Him. This is very true--and interesting, given that atheists will often say that we come to God out of fear. Whether or not that is ever true (it was not in my case) it is certainly true that we come to know fear. Fear is not the cause. Fear is one of the effects.
Sproul gives the perfect example from scripture:
3 Getting into one of the boats, which was Simon's, he asked him to put out a little from the land. And he sat down and taught the people from the boat. 4 And when he had finished speaking, he said to Simon, “Put out into the deep and let down your nets for a catch.” 5 And Simon answered, “Master, we toiled all night and took nothing! But at your word I will let down the nets.” And when they had done this, they enclosed a large number of fish, and their nets were breaking. 6 They signaled to their partners in the other boat to come and help them. And they came and filled both the boats, so that they began to sink. 8 But when Simon Peter saw it, he fell down at Jesus' knees, saying, “Depart from me, for I am a sinful man, O Lord.” (Luke 5: 3-8)
Peter was just getting to know Jesus. He was not afraid. He was even (possibly) a little condescending in an eye-rolling manner with Jesus. Ahem. Just who is the fisherman here? But OK I'll humor you, teacher. But when he saw God revealed he was so afraid that he had his personal Isaiah-6 moment, recognized his own unclean lips, and asked Jesus: please, just go away.