As someone who spent 15 years in the news game, there are a couple of things you should understand.
If the article (and accompanying photos) is still in the development stage, which many feature news type articles are, then the art director might just be gathering artwork at this time. Then he presents his article, photos, graphics etc., to the editor for final layout. Some of the photos will make it, some of the photos will end up on the editing room floor so to speak. This is not an unusual occurance. The reason they ask for the high-res scans, is that when the decision is made to GO, then at that point, time (no pun intended) is of the essence. If the images are already on hand, then the article can make deadline and go right to print.
There have been many times that I have sent out images only to have not made the cut, but then again, there are also many times when I have made it to print. That is the way the "game" is played. It's not unethical at all, even if you might at first think so. They will indeed PAY for what is published, but not for what is not used. Welcome to the real world. And you must remember to NOT take it personally. Sometimes it can be as simple a reason as the photo "facing" the wrong way left to right. So they go with the image that fits what the graphic artist has designed into the layout. Also, sometime an expected interview (for example with Northwest) falls apart and does not take place. Then artwork from Northwest is not as high on the list as for example artwork from American, where the expected executive interview actually occured.
It all sounds pretty complicated, but on average it generally works out about even. 50/50 on acceptances and rejections. But the payday for the acceptances generally makes the average work in the photographers favour.
This is the major difference when a photo is used to illustrate a feature or news feature article, as against an immediate news event.
So don't ever give up hope, shoot for your own satisfaction, and take the gravy when it comes your way.
p.s. I just recently had a photo from A.net picked up by PLAYBOY in Hungary. Nice to think that I am the feature (it was a photo of ME in a glider) subject in Playboy across a double page spread. Ok.... send me your witty comments
And yes.... I still had my clothes on.