When a patient presents with a set of symptoms, the doctor has to decide whether the patient has a boring common disease or the cool disease which is 100 times rarer. Human beings can't make good judgements about probabilities like that. If every doctor were trained to recognize a rare auto-immune disease that looks just like the flu, plenty of flu sufferers would be misdiagnosed. Far better to teach doctors the treat for flu and refer the cases that don't respond to a specialist.
It is a common problem with doctors fresh out of med school. Common enough that most doctors are taught to "not look for zebras when horses are more likely." If you spend enough time in a hospital you will hear veteran doctors dismiss interns and residents saying, "she's just looking for zebras."