I will usually prefer protagonists, though there are times in which I will prefer antagonists. With the exception of Otogi (he started off as an antagonist but later joined Yuugi and co., technically making him a protagonist by the end of the series), I despised or was indifferent to the protagonists from YGO (despised in the cases of Yami no Yuugi, Jounouchi, Honda, Shizuka, Anzu, and Rebecca and indifferent in the cases of Yuugi and Ryou). I greatly preferred the antagonists, since they had more interesting backstories and I could understand the reasons behind their actions (especially in regards to Dartz and Yami no Bakura/Thief King Bakura). Similarly, when it comes to Pokemon, I am a huge fan of the Team Rocket trio and greatly dislike Ash and Pikachu (as well as Misty).
There are also times in which I will like the protagonists and antagonists of a series equally. For example, I liked both the protagonists and antagonists of Fullmetal Alchemist on an equal level. The same holds true for Slayers and Steel Angel Kurumi.