So fun pieces of data:
In the first popularity poll Sakura placed 5th.
Of course, this was the poll given chapter 60. During the forest of Death. By the way, Hinata is already 10th by this point. Damn impressive considering her screentime consists of having a crush on Naruto and being willing to let him copy her test.
By the second popularity poll, right around the time of the Chuunin exam tournament (chapter 107), Sakura has dropped all the way to 14th!
This is a pretty big drop. Even if you just look at the number of voters (3055 vs 359). I guess all the cool characters introduced that got a chance to show off made their mark, while before we didn't know much about them.
By this point, Hinata has unsurprisingly (due to her fight with Neji) climbed up to 6th place.
By the way, Minato placed 12th. Not bad for a guy who only showed up as a stone monument and a picture.
Sakura actually beats Hinata in later polls. Not that hard since the latter barely appears.
Although in the last one (during the War Arc) Hinata is on top again.
Honestly, I'd say the problem is not so much Sakura not having fans but rather her also having a sizable group of people who dislike her. Meanwhile, Hinata haters were considerably rarer... until The Last at least.