Though she's beautiful and glamorous, Mrs. Coulter has no truly redeeming qualities. She's the head of the General Oblation Board (the Gobblers), the organization that's been kidnapping children in order to perform experiments on them. She's also behind the operation at Bolvangar, a facility that cruelly severs children from their daemons.
Are you wondering why we haven't listed Lord Asriel as an antagonist? Well, it's true that by the end of the book we find out he's not really a good guy – how could he be after the way he treats Roger? However, for most of the book, Asriel is not actively clashing with Lyra and getting in the way of her goals (rescuing Roger from the Gobblers, for example). That role is reserved for Mrs. Coulter. But there are two more books to come. We wouldn't be surprised if Asriel becomes a full-on antagonist in one of those. Would you?