Vaccines don't cure diseases; that's not how they work. They only teach your immune system how to fight the disease without exposing you to a lethal dose, which is why they give you a "weakened strain" or a "killed virus". Because of this, vaccines are almost never 100% effective. Sometimes they are so weak your body doesn't learn how to fight, or sometimes your body isn't capable of fighting. Some vaccines are only 40-60% effective. Efficacy also depends on other factors, including whether or not the disease you're exposed to is close enough to the antibodies the vaccine caused you to produce. And there are about 10% of the population who physically cannot get vaccinated, due to allergies or pre-existing health reasons.
In epidemic diseases, particularly those that readily mutate like influenza, it's hoped the vaccine is effective enough on enough people to keep the spread contained or manageable. A 90% vaccination rate is barely enough to convey herd immunity.
On the other hand you've got ignorant pop stars, preachers, and pandering politicians who promote non-scientific claims from a discredited researcher about vaccines causing autism in toddlers. By allowing those 20% of extremely stupid people to excuse themselves out of the herd, it's become tough to protect the rest of us. If the flu vaccine has only a 60% chance of protecting you should you become exposed, and the herd is unprotected, you still have a chance of dying from flu, even with a flu shot.
As for the rest of your post, there is a tremendous amount of experience and data on vaccines. They know the types of side effects, the rates of side effects, the rate of allergic reactions to the components, and can even predict the expected efficacy of each vaccine. They also know the expected mortality rate of the vaccines, and it's pretty easy to compare that to the mortality rate of the diseases they control. If the vaccine kills 1 in 3000000 people, and the flu kills 1 in 300 people (or 1 in 6, like the Spanish influenza of 1918), what do you think the ethical choices for a society are? Let the superstitious people kill off a bunch of us?