You can do it by putting the character in conflict with their environment -- and by that I mean it could be either the natural environment or the social and cultural environment. If a character is in conflict with society, it might not be that the society is evil or repressive. The other characters, in fact, might be kind and well-meaning, but ignorant. The role of the protagonist might be to enlighten them about the past, about the dangers they face in the future, etc. As with your scenario, it might be about different values, different perspectives.
You might write a story where the antagonist and the protagonist are both perfectly decent people but they have conflicting goals. If readers like the protagonist (and readers are likely to become partisans of the first sympathetic character they encounter in a story) then they will want him or her to prevail, even if the other character is not so bad as to be rightly characterized as a villain. And then there are romance novels, where the potential lovers might be in conflict, or there might be two people competing for the main character and neither of them a bad person, just one of them, ultimately, more appealing.
Of course there is inner conflict, and conflict with a character's own limitations. There are real-life stories of people who overcome their physical disabilities to become athletes, for instance, or other limitations to fulfill a role that is thrust on them (The King's Speech is a good example).