Some common ailments like the common cold of the flu have vaccines because the flu can be deadly (so I've heard) and because they're just plain annoying when you have to take a week off from work or school because your sitting in your bed and puking. We just wanted to stop getting sick. But as you know we still have not developed vaccines for cancer and AIDS and other un-preventable and incurable diseases. But we are working hard to create one. Hopefully in the next decade or two, mankind will make one. but for now we can only hope. Also, I found your question somewhat vague. Do you mean what is our reason or why SOME diseases and not all of them. If i took your question wrong, tell me and ill answer it as best as i can.
antibodies
Yes some do bring diseases but not all..
Genetic diseases Autoimmune diseases Some parasitical diseases.
we need protein for many reasons for a healthy body for better growth to prevent some nutrutional diseases thats kwashiokor
Bone eating diseases
not in general. maybe if you're camping. You need to get rid of them immediately some times they can carry diseases.
Children get some diseases from their mothers from their mother's mitochondria.
Some diseases were malaria and dysentery.
No. You will need to register your business. Some "pets" can carry certain diseases/germs that can transfer to humans such as cows. So depending on the pet you may need shots.
Trichinella, rabies, skin diseases
Circulatory system diseases, cancer.
some diseases caused by metazoa are pathogenesis and ddt