Even the beginner you tube videos I've found aren't any good though. They all seem to think that it's 'simple' to go from downward dog and 'simply' step one foot forward between your hands - I just can't!
Can you go to an in-person class? A good yoga teacher will offer all sorts of adaptations you can make. I can step from down dog to one foot forward with my right leg, but I find it harder with my left , so I do two steps. I can do some binds on one side, but not the other.
But in answer to your title, no-one is naturally bendy. It's gentle persistent practice, and stretching a little bit (to a point of mild discomfort if you want to) at specific moments in each session.
And yoga is weird - I'm 'bendy' in a civilian sense, but as a dancer (now very old) I'm actually below par on flexibility - I can do front splits but not box splits (straddle) etc etc. But in yoga, I look as stiff as a board! I can balance well in a pirouette position on my toes, but I find all the yoga balances really hard. So it's not about bendiness, it's about persistent practice. And gradually, your muscles learn. For me, my body is used to working in turnout, with specific muscles fired up to hold my leg at wait height & turned out. But yoga doesn't use turn out, so my muscles have to work differently to hold me up. I find it both frustrating and fascinating!
You could start by doing a more extended stretching session after your runs. I aim to stretch for 20 minutes after an hour of metcon training (heavy weights, followed by cardio) - I do that twice a week, in addition to yoga Pilates, and ballet. Can you add in some stretching after your runs?