From a purely statistical standpoint, vaccines are a no-brainer. But everyone has this one story about something going wrong. As a scientist, and from a personal point-of-view, I can comment on​ this.

For three out of the last ten years, I got the flu shot. Each of those years I got the flu. The other seven years, I neither got the flu shot nor the flu. Now is it possible this is entirely a coincidence? Yes. The flu could have just been worse those three years, or I could have got lucky or unlikely, as you may.

I also understand that it is sometimes difficult to predict the exact effects of injecting genetic material into the body. This concern is why genetic-based medicines have not moved forward as fast as promised. The delivery paradigms can be challenging and require significant individual optimization of dosing for meaningful effects.

So from a scientific viewpoint, there is always uncertainty. Part of the challenge is that too many people on all sides seem to have way too much certainty. It's always best to express in terms of real statistics. In the case of the flu vaccine, the statistics aren't generally great. Between 10-60% effectiveness each year. Most others are much higher.