If I recall correctly, it's because back in the day (15th/16th century), university academia was not as specialised. If you went to university, you studied philosophy and became a thinker. Regardless if you focused on maths, physics, biology etc. there was an emphasis on a broad education, to become a 'learned man' in all aspects. Even when taking something to doctoral level, you would have continued with philosophical discussions with other academics. It still is called that because as with most things academic, tradition is very important. The exception now, of course, is an MD for medical doctors. (no source I'm afraid, just one of those random bits of info floating around in my head. Hope this has been slightly useful!)