I remember learning how to combine rhythms "intellectually". At Juilliard, we eventually used Robert Starer's "Rhythmic Training" book, but that quickly advances to quite complicated stuff which is probably unnecessary for most people's purposes (The percussionists and the jazz players were really good at it).
Then there's "feeling" rhythm, which at least to me is far more important in the performance of music, especially with other people. I have a feeling much of it is instinctive, communication back and forth between performers, a "groove", so to speak. If you don't have other people to practice with, you can certainly try playing along with recordings, but it's great to have instantaneous feedback.
If you're playing solo music, a lot of it is natural in the sense that you can't force it, it's not mathematical. Think of how jazz "swing" can't normally be notated using the standard Western system. People playing Western "classical" music also employ a swing or an unevenness, or a rubato, whatever you call it. If the player doesn't have it, it sounds really stiff and stilted. Again, in my experience, relaxation is the key, and not worrying about the end result is part of that. True, some people appear to have more of a natural rhythmic gift than others, but I think unless you're attempting to do something pretty complicated, most humans are capable of something which will sound musical and communicate some sense of drive.
(my opinion only, of course)