I think things are getting better, in at least some churches; I'm starting to see procedures in place for preventing the sexual abuse of authority and reporting it when it happens.
But thinking back over the sex education I received in church and Christian-school settings: There was lots and lots of emphasis on avoiding premarital sex. In church youth group, in college-age youth group, in the sex education classes at my Christian school. Amongst ourselves, we invested a lot of energy in figuring out just how "far" you could go before it crossed the line. In all of that, though, I don't remember any attention being given to the idea of people in authority abusing that authority in sexual ways.
The first mass-market information campaign that I saw about this issue was the "My strength is not for hurting" series of posters. (If you didn't see them, they were posters that showed two people in an affectionate pose, with a caption like "So when I wanted to and she didn’t, we didn’t.") The first time I saw one of those posters, I cried. I was well into adulthood, and these posters came from a secular source, not any church.
Maybe the trouble is that if the whole focus is on preserving virginity, all non-marital sexual acts get lumped into the same "immoral" bucket, so that consensual premarital sex and sexual predation by clergy are considered equally bad; thus, sexual predation is seen as no worse than a couple of college students having consensual sex. I think this is the attitude I grew up with. The article touches on this problem.