I encourage people to think critically about vaccines (just like any other topic). However, pseudoskepticism about vaccines (just like any other topic) is harmful because discouraging others from vaccinating leads to a rise in, for example, whooping cough. Orac has also written about the rise in measles in the wake of decreasing vaccination.
Remember, the decisions you make about vaccination affect others as well. Some critical thinking about vaccines is good -- for example knowing when to go ahead or delay a shot due to illness (or knowing what conditions may lead to a life-changing reaction). However, a blind rejection is as bad as blind acceptance.