Maybe it isn't the "best" one, even in my own opinion, but that's talking in terms of if I were to try to look at these games in a vacuum. But there's no fun in that, and it doesn't reflect how people evaluate things in reality. Even if I can convince myself that it's not the "best", it's undeniably still my favorite and the one I most enjoy coming back to. In that sense, it kind of is the best, at least as far as my evaluation is concerned. And obviously I'm not the only one who feels that way if the poll results are any reflection.
I don't blame people who don't like it though, because I feel the same way about supposed "greatest ____s" that I don't personally care for. It's easy to dismiss those biases when you don't care for something, because they don't exist, but if it's something you like they definitely affect your perception.
Imo, Twilight Princess would be the best one if it wasn't for those wolf segments, slowest start to any Zelda game. Skyward Sword would have been the best if it didn't have those buggy motion controls. Wind Waker is pretty good but the art style is too different. I don't even know if Breath of the Wild counts as a Zelda game.