I'm a family physician with over 15 years experience. I also serve on our county's Board of Health. I haven't been very active on these boards for a while.
IMO, antibiotics should NOT have been prescribed for a non-streptococcal pharyngitis/tonsillitis. IMO, this is an indication that your doctor would rather do the convenient rather than the correct action. It can take a long time to convince people that they will get better in 48 hours with the antibiotics or in 2 days without. Too many doctors find it is easier to just prescribe. However, there is good evidence to suggest that antibiotics are much more likely to be harmful (drug allergies, antibiotic associated diarrheas, yeast infections, decreased birth control pill effectiveness, antibiotic overuse) than to have any benefit for this disease.
In addition, it is now being discussed whether strep throat even needs antibiotics. Strep usually gets better on its own in about 5 days. Antibiotics will shorten the duration of the illness if given within the first 2 (maybe 3) days. The primary reason that antibiotics were so strongly recommended in the past was to try to prevent the most feared complication of strep throat - rheumatic fever. However, the strains of strep which caused rheumatic fever have been largely eradicated. There has not been a large epidemic of Rheumatic Fever since 1980. There are other complications from strep (particularly glomerulonephritis and abscesses) but antibiotics have only a minimal role in the prevention of these. As a result, physicians who are concerned about the overuse of antibiotics are now starting to discuss NOT using antibiotics.
Such concerned physicians already have learned to not prescribe antibiotics for most cases of bronchitis (particularly under a week's duration). Most physicians are now adopting recommendations to not use antibiotics for children with ear infections (unless the child has a fever >102F). I predict that strep is next. (This assumes that the patient has been vaccinated. Vaccines now prevent the great majority of serious infections for young people). I try to follow these recommendations and only modify them for people with serious underlying diseases (particularly diabetes and poorly controlled asthma).
BTW, Influenza is one of the few bacterial infections for which antibiotics (tamiflu, relenza or amantidine) are effective to shorten the duration of the illness. However, these should primarily only be used for the sickest people.
Strep is most common in the 6-10 year age group (at which time ~50% of sore throats are strep). By the time people get to age 30, only ~15% of sore throats will be caused by strep. I usually educate my young patients' parents that if their child has a sore throat, they can call up and ask for an order for a rapid strep screen. If it is negative, they don't need to have an office call. I also strongly educate them to avoid ANY exposure to tobacco (even from clothing from parents who allegedly smoke outside).
I hope this has helped.