Although natural products can be toxic and dangerous, the ones that are actually used in pharmacy are "the lesser of two evils". Generally, the natural products intended to be used in pharmaceutical formulation are low toxic and cause fewer adverse reactions. Obviously some of them can be incompatible in certain cases (renal dysfunction, pregnancy, etc.) and with certain medicines.

Generally (again), they are easier to produce (sometimes cheaper too) and more stable than isolated/synthetic carriers. And, most of times, natural products contain several phytochemicals that can improve bioavailability, offer synergistic effect or simply improve overall performance of the formula (for example soothing effects for a dermal API that usually causes irritation).

There is no absolute winner. That's why each case has to be carefully considered, selecting the best carrier/compound amongst all possible choices (both natural, isolated, synthetic) and of course, taking into account the desired specifications of the product, patient's needs, budget, etc.

They are products of biosystems and compatible with majority of biochemical reaction, pathways and products of primary, and secondary metabolites. The receptor affinity is of prime importance for a natural product to bind and produce effects, the choice of the receptor or exactly the natural products pharmacophore fitting the receptor type will produce the effects the receptor is responsible for. Not all natural products bind to many receptors, rather specific in nature. Multivalent binding and specific receptors produce their effects, at times harmful as their intrinsic property.