We are muscle and sinew, tissue and bone, blood, sweat, and tears. Complex, extremely complex systems and parts operate these bodies of ours, complex beyond absolute understanding. Some of our physical malfunctions are pretty straightforward and easily explained. What isn't so simple is knowing how much time is needed to heal, what the most effective method of treatment is, when to say everything is back to normal. And often diagnosis is far too simplistic, misleading, or too convenient.
What I'm saying is that you may have cold symptoms but you learn from experience how far you can push through without taking time off from training. If you have a sore ankle, it may not be enough to stop you. You can certainly make mistakes, just as doctors can be off in their diagnoses.
To complicate matters, and as everyone knows, your mental state has an enormous effect not only on your approach to fitness and health but on your actual physical health. Mental and emotional stress, for example, greatly affect the healthy function of your body. It's almost like stereo feedback sometimes; is the mental angst causing the physical problems, or vice versa, and how do you stop the mad spiral?
Running helps to reduce stress. Reduced stress affects physical and mental health positively. Cardio health, muscle and bone strength... the list goes on and on. So even in complexity there are some pretty clear signs.