Cephalosporin, another powerful antibiotic, was first isolated from a mould found growing by a sewerage outlet in Sardinia. It is easy to understand why a mould growing in that location would have a need for a powerful antibiotic.
No fewer than 49 different natural pesticides have been identified in cabbage, for instance, including chlorogenic acid and allyl isothiocyanate, which, in addition to being toxins, can mutate DNA. There are also sinigrin, carvone, indole-3-acetonitrile, nitroso indole acetonitrile, caffeic acid, and organic cyanides. These toxins, which, molecule for molecule, are just as poisonous to humans as pesticides used in agriculture, exist in far greater amounts than are permitted for their synthetic counterparts.
Another point made is that the reason why chemicals extracted from natural sources can be so useful is because they're the product of millions of years of ruthless evolutionary optimisation, and not because they carry Mother Gaia's blessing or anything like that.