It's mostly historical. Gregorian Chant was written without much thought given to keys or the like; it was melodic only, but there were traditional composition procedures. Later, people tried to classify chant as to its characteristics; some chants were clearly related in style and form. This procedure gave rise to eight modes comprising four ending notes (D,E,F,G) and ranges basically D-D or A-A and E-E and B-B and F-F and C-C and G-G and D-D. Amusingly the note Bb was in existence by the time this classification was made. The F mode sometimes had a Bb which made it equivalent to a (hypothetical) mode on C.
As music underwent changes, more modes were suggested and pieces could have parts written in other than their beginning modes; this led to the addition of more notes like Bb (Eb to start with, etc.) In parallel with this was a 6-note pattern called the Hexachord system (it's worth reading the Wiki on hexachords. It's complicated and more so when combined with the chant modes,
During the 1300-1500 time frame, harmonic concepts were expanded into the current scheme used now, but not with the same usages. The chords (triads anyway) were known and used but a good description wasn't available. The musicians (as usual) outran the theorists.
By the 1600s, it was clear the that modes on D and E (as then used) were characterized by the having a minor third (D to F and E to G respectively); the modes on F and G were characterized by having a major third (F-A and G-B) similarly placed. It was recognized that modes on A and C were also becoming common.
Because of the above characterization of the modes, those with a minor third at the beginning (A,D,E) were termed minor and those starting with a major third (A,F,G) were called major.
Composers also found that the distinction between major and minor was greater that that between other possible modes.