When the Scooby universe was first created, Fred was given blond hair. His hair stayed blond for all of the animated Scooby shows and the live-action movies starring Freddie Prinze Jr.
Then came the live-action prequels in which Fred was given brown hair.
So, why was Fred's hair color changed for the prequels?
States TV Tropes, "Fred is normally a blonde but in this movie as well as the sequel he has black hair. A deleted scene from the 2002 movie reveals that he dyed his hair."1
According to TV Tropes, the prequels take place in an alternate continuity2, which TV Tropes defines as "a story that is no less 'official' than the original, but which cannot be reconciled with it with regards to backstory or canon. It effectively lives in a different universe."3
In a Los Angeles Times review of Scooby-Doo! The Mystery Begins, television critic Robert Lloyd writes, "Purists will note that Fred's hair is not blond -- perhaps he began dying it later."4
If the show A Pup Named Scooby-Doo is canonical, then Fred must be a natural blond, because it is highly unlikely that a boy still in elementary school would have been dying his hair on a regular basis.
Keep in mind that if A Pup Named Scooby-Doo isn't canonical, then What's New, Scooby-Doo? isn't canonical, either, because the latter features a reference to the former.5
Information Sources:
1Scooby-Doo! The Mystery Begins. TV Tropes. Retrieved from https://tvtropes.org/pmwiki/pmwiki.php/Film/ScoobyDooTheMysteryBegins
2Ibid.
3Alternate Continuity. TV Tropes. Retrieved from https://tvtropes.org/pmwiki/pmwiki.php/Main/AlternateContinuity
4Lloyd, R. (2009, September 11). Scooby-Doo! The Mystery Begins. Los Angeles Times. Retrieved from http://articles.latimes.com/2009/sep/11/entertainment/et-scooby-doo11
5A Terrifying Round with a Menacing Metallic Clown. What's New, Scooby-Doo? https://www.watchcartoononline.com/whats-new-scooby-doo-episode-36-a-terrifying-round-with-a-menacing-metallic-clown