i tasked my assistant, Hubert, with interviewing an official* from my local Public Health Department concerning the safety of the vaccines that they routinely administer
she stated that there are, indeed, side effects that can be experienced with nearly all vaccines
however, the incidence of side effects is extremely low - there is as much risk of being struck by lightning. you are far more likely to be injured or killed in an automobile accident than you are of contracting a serious illness from a vaccine. perhaps we should stop driving.
there are also far, far more studies by qualified researchers - peer reviewed and vetted - that establish the safety of vaccines than there are credible studies indicating an unacceptable level of risk (the often-cited study linking the MMR vaccine and autism was fabricated, and the man who published it admitted this in a public news conference, but people still wave this one around)
of more concern is the effectiveness of many of the vaccines currently in use. the problem there is that while the number of virus and bacteria strains continue to grow and mutate, the pharmaceutical companies have not kept pace in research and development to produce vaccines to counter them - the reason being that it is not very profitable for them.
but for communicable illnesses, such as the flu, even preventing one person from contracting the virus prevents the spread of the same virus to unknown number of people that they might come in contact with - each incidence of success has an immeasurable ripple effect. so even if the vaccine isn't 100% effective in stopping the virus in everyone who gets the shot, it still makes a considerable impact.
as far as there being some sort of government cover up - anyone who has ever worked for a government agency knows that they are best at grinding away very slowly, deliberately, and cautiously, and spend more time producing paperwork to protect themselves against an overly litigious public than they do actually making any real progress.
oh, and she said the best way to combat disease is to wash your hands frequently and keep from touching your face
*my girlfriend, a Registered Nurse for 30 years