I know you’re just metaphorically saying that some people seem to “just know” this stuff, but I feel the need to point out that it’s impossible for someone to be born with the ability to put words to rhythm, since we are not born with any vocabulary 🙂
But on a less pedantic note, I believe it’s actually an acquired skill that we pick up – perhaps some pick it up unconsciously and appear to have a natural knack for it, but the mechanism is the same. To me it’s the same way that someone who’s read a lot of fiction, will have a leg-up when it comes to writing fiction. They’ll have been exposed to so many different writing styles, they’ll have a natural feel for how to emulate that.
I think that if you consciously apply the techniques outlined in this lesson – e.g. listen to some of your favourite songs and look at how the lyrics have been placed in relation to the rhythm – you’ll catch up with those “naturals”.