Penicillin may fail to work because:
• presence of beta-lactamase producing bacteria that "protect" strep from penicillins
• absence of bacteria that interfere with the growth of strep
• co-aggregation between strep and Moraxella catarrhalis
• poor penetration of penicillin into the tonsillar tissue cells which allows intra-cellular strep and Staphylococcus aureus to survive
Indeed, in the treatment of recurrent and chronic strep throat, clindamycin or amoxicillin-clavulanic acid (augmentin) can eradicate both aerobic and anaerobic beta-lactamase producing bacteria as well as strep itself. Cephalosporins and clindamycin have superior intracellular penetration which enhances their efficacy as well.
One also needs to keep in mind that there are OTHER germs that can cause infections besides strep like Fusobacterium. More info here.
Of course, if a patient has suffered from such severe and recurrent strep infections, it just might be time to remove tonsils and adenoids surgically.
Penicillin failure in the treatment of group A streptococcal pharyngo-tonsillitis: Causes and solutions. Journal of Pediatric Infectious Diseases. Volume 8, Number 2 / 2013 Pages 59-69