I think it's more to do with preferences in certain characters, their design, their backstory, their weight in the story, their abilities, etc. If people are just rooting for characters because they will win in the end then I think they are looking at it the wrong way. I mean sure, you can root for the good guy, but there has to be more than just rooting for them because he will win.
Only reason why I usually root for some villains is because most of the time they have better techniques, they are more interesting to watch, their character designs are more appealing(subjective), and they bring conflict to the series.
Most of the Akatsuki were immortal or had some OP ability. Madara, Sasuke(when he was an antagonist) and Obito both had their own ideals and they brought Shippuden to it's peak because they went against what the good guys believed.
It's not really rooting for a character because of the outcome or the victory, more so because you like said characters, which is why Madara has such a huge fanbase.