"Doctor" is a formal title: it refers to a person with a doctorate, whether PhD and MD (the most common), or more specialized degrees like DDS (Doctor of Dental Surgery) or EdD (Doctor of Education). Isaac Newton was not called Dr. Newton for the simple reason that he did not have a doctorate (the same way we would not call him Senator Newton for the simple reason that he did not belong to any senate). Newton did have a Bachelor's and a Master's degree, and he later became a professor (another title he could use), however he never pursued a doctorate.

Regardless, the title "Doctor" has never been exclusively associated with medicine.

Associating "doctors" primarily with the medical profession is actually a fairly recent phenomenon, mostly resulting from medical doctors being the ones that an average person is most likely to interact with. The term"doctorate" goes back almost 1000 years -- long before modern medicine was a thing -- and was initially associated with academics, teachers, and other people of knowledge (the term itself is Latin for "to teach"). The first formal doctorate was given in 12th century Paris, and even that is only from a European perspective; some trace it back even further to the 9th century Madrassahs and their equivalent doctorate of Islamic law ("ijazah"), those others have disputed whether these two titles are equivalent. Regardless, the term has a long history of indicating a person who has obtained the highest degree of knowledge, and is thus qualified to teach others. In ensuing centuries (again, this is largely European), doctorates commonly came in three flavors: theology (ThD), law (JD) and medicine (MD). The modern usage as the highest academic degree goes back to the early 19th century, when formal university educations of the modern variety started to become standardized and the formal doctorate was re-introduced in Germany, and then spread throughout Europe. But even here, it was a research degree (equivalent to today's PhD) rather than a medical degree (a degree for practicing a trade -- namely, medicine).

There are some claims (though I cannot substantiate these) that early medical doctors (MDs), who were practitioners rather than researchers (PhDs), began foregrounding their "doctor" title in order to gain more legitimacy, as the "doctors" of academia (the ivory tower and whatnot) were more highly esteemed, however this very well may be apocryphal. I only mention this because the story does convey the fact that academic doctors (researchers and teachers, those affiliated with institutions of knowledge) were already well-established before modern medical doctors.