Why my 3 month old has blood in his stool?

my 3 month old has been diagnosed with rsv since new years eve. I have been giving him breathing treatments along with antibiotics since then. Yesterday he was not feeling his best at all. He seemed as if he was having difficulties breathing because he was so stopped up. I took him to the emergency room so they could check his oxygen and they said it was at 100% which is good. this morning when i changed his pamper he had blood in this stool. he wasn't constipated, his bowel movement was very loose with a lot of blood in it. I immediately called his dr and brought him in. he told me my child was fine. the blood in the stool was coming from his antibiotics. his antibiotics are white. my child has not had anything that has red in it. he barley wants his milk because he cant breathe out his nose. he is very congested in his chest area. if he has been doing his breathing treatments 4x a day for a week now, shouldn't he be improving by now? and where would the blood be coming from? I have heard so many complaints about this dr that he is not good and will send your child home regardless of there situation. what should I do????