The word seminar is relatively new in the language. The modern business sense ie a conference for specialists, or course of instruction for businesspeople dates back only to the 1940s. The university-related sense dates back to 1880s, when it originally referred to the method of tuition in German universities. The first definition at the OED entry is: "In German universities (hence in certain British and American universities), a select group of advanced students associated for special study and original research under the guidance of a professor".
Seminar developed from the earlier word seminary, which nowadays usually refers to a college for Roman Catholic priests. The origin of the word seminary (and hence seminar) is the Latin seminarium or seed-plot, and the earliest definition in the OED is: "A piece of ground in which plants are sown (or raised from cuttings, etc.) to be afterwards transplanted". The meaning then broadened to include "a place where animals are bred", then "A place of origin and early development; a place or thing in which something (e.g. an art or science, a virtue or vice) is developed or cultivated, or from which it is propagated abundantly" (OED) and then "a place of learning", or "an institution of training for those destined for a particular profession." The OED tells us that in the first half of the 19th century private girls' schools were often called "seminary for young ladies" or "ladies' seminary".
It's interesting that the word seminary was used with reference to girls' schools. No-one seems to have any problems with seminar or seminary these days, but the same cannot be said about the similar-sounding words with a related etymon seminal and disseminate. These words both derive from the Latin semen, seed. For this reason, some people and organisations feel that the words seminal and disseminate are sexist. The British Sociological Association, for instance, recommends that they be replaced with classical or formative (seminal) and broadcast, inform or publicise (disseminate). You can read the BSA's document entitled Language and the BSA: Sex and Gender by clicking on the link on this page.