I feel this question deserves a shorter, more to the point answer:
Because when they decided to name the notes with letters, they took a minor scale and named the notes "naturally": A, B, C, D, E, F, G. This is what we know as the A minor scale.
(CONTINUED EDIT:)
Therefore the choice of names was accidental - it just happened that they considered a minor scale instead of a major one. Now if we want to use the same "natural" notes in a major scale, then we need to start with C.
If, however, we were to turn back time and influence the early notation to use a major scale as a basis, then they would name "A" the first note in the natural major scale, and then today we would talk about A major as the "standard" scale. But of course this "alternate" A would be the same frequency as "our reality" C.