Simply because vaccination (for one particular disease) isn't always 100% effective does not refute the evidence that vaccination overall has been enormously effective and reduced the worldwide disease burden tremendously. If you want an example of that just see the eradication of the smallpox virus.
Your logic is akin to saying "this particular drug didn't work in a few cases, therefore all drugs don't work ever". I think even you can see how silly that is?
