I've been reading a lot of fiction this summer. In my opinion the protagonist is the most important thing in any story. Yes, that includes speculative fiction stories. There are some different ways to achieve an effective protagonist...
Probably my favorite type of protagonist is a flawed but heroic protagonist. This is someone who tries to do the right thing but has some significant personal issue(s) that will make this difficult. This type of protagonist is very common in YA fiction and is very easy to empathize with. Often they also have a unique characteristic, like a supernatural ability, or extra gumption or brains or something similar. In modern fiction, there's a sliding scale of flawed heroism that goes all the way to the anti-hero. An anti-hero would be mostly (all?) flaws--but still opposing the villain.
Please note there's an important point here. In most cases, an empathetic protagonist should have at least one good quality. (Yes, fighting evil could be that quality.) An effective author tool to make readers empathize with a protag is to show other characters caring about said protag. Or, you could have said protag experience something bad, like bullying. Or, you could have said protag caring for babies or puppies. :)
In the olden days all protagonists were straight-up heroes. They are basically perfect and always fight evil and win. You shouldn't use this type of protagonist because it's too old-fashioned. Modern folks can't identify with perfection.
I read a novel recently in which the protagonist basically had no flaws or problems. I did not enjoy that novel!
Of course, the polar opposite of a hero is the villain. They work to oppose the hero. Again, there's a sliding scale here. He/she could be an old-fashioned all-bad villain all the way to a partially good-villain. What makes a villain? That can be hard to decipher in this day and age. I'm going to say villains pursue evil while heroes pursue good.
There is an interesting modern phenomena in which stories and novels are written in which the actor has no, or very few, redeeming qualities. Basically, the author has made the villain into the protagonist. The fiction of Gillian Flynn might be an example of this. And you can't argue with success! Therefore, one way to create an effective protagonist is to actually create a villain. Who knew? :)
Good luck with your protagonists!