A plane could crash and a car could crash. One method of travel is still safer than the other.
It may very well be that this particular vaccine caused new health problems in some (likely small, but non-negligible) part of the population, and that the trade-offs involved still weigh heavily in favor of vaccination.
Absent mindless "if you aren't with us, you're with the terrorists" thinking, one might hope that the negative health impacts would be investigated and mitigated to further improve the vaccine technology.