Many reasons. 1) Several diseases we know now, are caused by non-bacterial microbes, therefore antibiotic (abx) are ineffective, 2) Using a lot of abx have led to the development of multidrug-resistant bacteria 3) Very little new abx are being developed due to costs associated to get government approval to use it, 4) We now appreciate that serious infections and side effects can occur with abx use.
Resistance. Potential for resistance, most cases don't require it, and/or side effects when you don't need it.
Antibiotics. The history of large amounts of prescribed antibiotics has led to the emergence of dangerous bacterial strains with antibiotic resistance. More cautious prescribing and fewer antibiotics for non-serious illnesses has started to control this resistance. Furthermore, use of focused, as opposed to broad-spectrum antibiotics has helped to limit (to some extent) the emergence of resistance.