Antibiotics are medications that fight infections caused by bacteria, but the flu is cause by a virus. Taking antibiotics when you have a virus may do more harm than good. Taking antibiotics when they are not needed increases your risk of get ting an infection later that may resist antibiotic treatment.ntibiotics only cure certain infections due to bacteria -- and if taken carelessly, you may get more serious health problems than you bargained for. With any illness, it is critical to address the underlying cause, whether it's bacterial or viral.