I think there is some official art for the original games that has Link as a blond, it's just that in the acual game sprites, it's brown because it's all they could do at the time. In A Link to the Past, he's PINK of all things in the game sprite, whereas official art has him as blond - they were probably trying for a "strawberry blond" then.
Then there were the early 90s American cartoons that had him as a dark brunette. Perhaps Nintendo was trying to differentiate from those? Maybe once Ocarina of Time was in the works, they really wanted everyone to know "this is a different Link. BRIGHT YELLOW HAIR!"
I like it, myself. I'm a blonde. Blond ambition, baby! I wouldn't mind if they changed up his hair a bit in the future, though. I think a Link with long (to the center of the back) black hair would look quite good.
*blond vs. blonde. "Blond" is the male term, "blonde" is the female term. Yay weirdness in the English language!