Somewhere in the middle. Honeycrisp apples are a combination of naturally occurring genes, but they are propagated clonally and in fact cannot reproduce true to themselves. They'd never have arisen without careful cultivation, and (this part is important) another group crossing the same original cultivars as the developers of the honeycrisp used wouldn't get the same apple. So it's a combination that is unique to its inventors, rather than a patent on something anybody could do - and nobody will infringe by accident.

An example of a bad patent would be a patent on a process anybody trying to solve the problem would come up with - that's a needless restraint on trade - and an example of a truly horrible patent would be one on a human gene. Those existed until 2013, when the supreme court finally ruled against them.