Great job explaining why most bacteria are not harmful. Another factor making bacteria seem more dangerous than they are is our current nomenclature system. E. coli, for example, has a ton of sub-species that vary in effect on humans. Some are beneficial (like the vitamin K producers you mentioned) while others are pathogenic. Often any pathogenic strain is called E. coli without making a sub species distinction which can skew perceptions on how dangerous all E. coli species are.