Isn't it obvious? Hinata's popularity is all thanks to Sakura.
Whether you agree or not the fact of the matter is Sakura was very annoying at the start of the story. Her Sasuke fangirlism and her initial treatment of Naruto made a lot of fans hate her character. The anime team did not help matters as the exaggerated Sakura's behavior for comedy. Even though sakura changed, the damage was already done.
Hinata is basically the polar opposite of Sakura (and all the other females for that matter) and because she had a crush on the main character which a lot of people consider to be cute, that ultimately made her more appealing to the fandom. The anime also doing all the Hinata fanservice played a huge part in Hinata's rise to popularity.
Because a lot of people hated Sakura (the female lead), they moved on to the next best thing which is Hinata (her feelings for naruto is what made her stand out fro the other females).