The idea is that by using natural family planning you are not doing anything in the process of the act itself to stop conception. In other words, even if you were trying to have a baby, you would be doing nothing different if you had sex on whatever days you have it while using the natural family planning method. The Church has never said you can't have sex on certain days or that you can't have sex if you happen to be infertile due to an illness or whatever, because you are open to life in the actual process of the sex act, and it is exactly the same as what you'd be doing other more fertile days or if you were fertile in general.
What the Church is saying with condom use is that it is specifically changing what happens during the act itself versus what you'd be doing if you were open to having a child. It changes the basic process and symbolism of what is going on in some respects.
Having said that, NFP is not intended as a permanent approach, but something to be used under select circumstances. There is a question of substance as well as form, and that's why you'll notice the wording of some of the documents on the subject are conditional and don't encourage the idea of NFP for everyone or for use on an indefinite basis.
For obvious reasons, this is not the most popular stance the Church has ever taken, and it doesn't help that it's often very poorly explained. The simple explanation and talking points that are passed around often give the wrong impression because they don't get to the heart of the issue or go off on kind of a tangent. What the teaching is really getting at is kind of subtle and complex, which unfortunately is tough to convey in a soundbite, and thus beyond a lot of people's attention spans.
I'm not trying to get involved in advocating for a point of view specifically, I just thought I could shed some light on what the Church is thinking.