Why two protagonists here? Well, it's all part of the trickiness of a love story that places the two participants on fairly equal footing in terms of the narrative – which one do you side with? In this story, we'd really say that it's a matter of perspective. Clym has the shout-out in the title going for him (he's the "native"), but Eustacia kicks-off the novel for us. And while Clym is largely absent from the start of the story, making it more Eustacia's, Eustacia is dead and gone by the end of the story, making it more Clym's. So we'd like to propose that both of these characters are protagonists. We sympathize with both and root for both. And even when they are arguing with each other, we kind of want them both to win somehow.
If we go with a strictly traditional point of view, then Clym is probably the official protagonist – he is the hero who ties all the other characters together and whose story drives the narrative. But there's a strong argument to be made that Eustacia is in fact the real protagonist of the story. She also drives the narrative, she's featured very heavily in the story, and the narrator sympathizes with her and focuses on her a great deal. In fact, in an 1878 letter to his illustrator Arthur Hopkins, Hardy describes Clym as the most important character of the novel, but Eustacia as "wayward and erring heroine" (source). So if we can only have one protagonist, then who is it? It's up for debate, we say.