I am totally open minded about this topic, but I didn't find that article particularly convincing. The general point is that you are exposed to millions of harmful pathogens per year; a vaccination is just a few more, so .00000000000x% increase.
But, this is assuming that a vaccination is in no way different than normal pathogens, which I have no way of knowing.
I have heard both anecdotal, as well as confirmed (I am quite sure) cases of children dying within very close proximity to receiving certain vaccinations. I think I have heard of 3 Canadian (or was it US) girls getting sick and dying within days after receiving the new cervical cancer vaccination.
Now, maybe I can't prove that it was the vaccination that caused my daughter to die 3 days later, but sometimes recurring coincidences sometimes indicate something is happening outside our sphere of knowledge.