I don't believe that there is an argument that vaccines are an overall net negative to public health. However, it does bother me that some folks try to sweep vaccine reactions under the rug as if they don't exist. It also bothers me when doctors who point out the risks are verbally tarred and feathered.
To me, when you consider any medical intervention, any medical intervention at all, there are always risks and side-effects. Even common drugs like aspirin that are widely regarded as safe may sometimes cause lethal reactions in a few patients. That is not to say that they are bad drugs.
To see the big picture, you have to look at the benefits of the therapy and compare them to the risks. Robert Sears has written about this in his "Vaccine Book". He has pointed out that he has concerns about the safety of vaccine ingredients. He also points out objectively how many cases of infectious disease have likely been prevented by vaccination. (I've noticed that most writing about vaccines, whether for or against, descend into personal attacks against people with whom the author disagrees. Robert Sears seems to be one of the few authors to present objective facts about personally attacking others)
I would like add further that vaccines are quite different from one another in terms of the ingredients used and how they mare made. Some contain live pathogens; some contain dead pathogens, some contain fragments of dead pathogens. Some contain trace amounts of toxic chemicals, such as aluminum, to enhance the body's immune response to the vaccine. In short, asking "Are vaccines safe?" is like asking "Are pain pills safe?" Each one has a different profile of risks and potential side effects.