Both sentences are indeed very similar and are pretty much interchangeable.
I’d say a subtle difference is that “il est bon” covers something very general while the second sentence sounds more like an advice given to a particular person. With “C’est bon” the sentence for saying something very general would be:
C’est bon de faire de l’exercice tous les jours.
Both of these sentences sound a little odd, especially the second one. I would modify them this way, and add a couple of variants:
(a) Il est bon pour votre santé que vous fassiez de l’exercice tous les jours.
(a’) Il serait bon que vous fassiez de l’exercice tous les jours.
(b) C’est bon pour votre santé que vous fassiez de l’exercice tous les jours.
(b’) C’est bien que vous fassiez de l’exercice tous les jours.
and here is how they could be interpreted:
(a) and (b) are statements, whether the listener exercise daily or not is unknown.
(a’) is an advice, the listener doesn’t exercise enough yet.
(b’) is a congratulation, the listener does exercise daily.
For me, using “Il est” instead of “C’est” sounds very formal, you could write it but it sounds weird when said, even though both refer to a general fact. “C’est bon de […]” is much more natural.
Then I guess it depends on where you come from, just as the difference between “C’est quelle heure ?” and “Il est quelle heure ?” : for me the first one is natural and the second one is a bit less colloquial, whereas for some people the first form does not exist and they always use the second one.