To all the pharmacology savvy?

Flu is a viral illness, not treatable by antibiotics. However, perhaps your doctor observed something in your clinical picture that led him to believe an antibiotic was in order. Different antibiotics affect different types of bacteria. It is probable that he thought you had something that was treatable by Doxycycline, that would not be as well treated with Penicillin. Frankly, Penicillin is rarely called for these days because MOST bacteria have developed resistance to PCN. Doxy is a newer drug, effective against many organisms that USED to be treatable with PCN. That's almost certainly the reason he prescribed as he did. If you have further questions, you REALLY need to address them to the physician. He examined you; we didn't. He knows what might be making the rounds in your area; we don't.