From what I have read about this whole issue, it is certainly much more complex. Yes, antibiotics overuse in factory farming is certainly dangerous in that it can create antibiotic resistant strains of bacteria that we at some point cannot control. There are also huge problems with viruses in factory farming. Generally it isn't a good idea to have so many animals close together, it gives much more opportunities for diseases to spread. Especially because the animals that are used have an incredibly low gene pool and are maximally stressed I'd assume.

But another opportunity for diseases to jump from animals to humans is wild animals. By destroying more and more natural habitats, people also get in closer contact with wild animals. Like covid 19 most likely spread from wild animals to humans. So, habitat and biodiversity loss are also important risk factors increasing the potential for diseases to cross over to humans.

In my opinion, we should stop keeping animals altogether, as well as plant monocultures and should try to conserve as much habitats as possible.