A case can be made that Cloud and Aeris somewhat share the role of "protagonist" in the story, given the significance they bring to the primary conflict, which is Sephiroth vs the world. Tifa doesn't have as direct of an arc tied to this conflict, as her story is more to do with Cloud and his internal struggles. Tifa doesn't really have much of a leg if it came to a discussion as to who fulfills the role of "protagonist" more.
From a look at story-structure, Cloud and Aeris' equal roles in the central conflict makes their characters serve as strong foils to one another as much as anything else. This is very similar to the way FFX does it with Tidus/Yuna. This structure continues to exist outside of Aeris' role of being a love interest for Cloud, and continues to exist after she dies. I would argue that the nature of the structure/conflict/role fulfillment doesn't say too much about the role of Cloud's love interest, as there is another option there. If, hypothetically, Yuna had a version of male!Tifa in FFX (or FFX-2) and Tidus didn't come back to life, I would say the same thing.
Cloud/Tifa don't really have that same type of comparative structure to their arc, by nature of how Cloud is the focus of the conflict. I think the argument could be made that by giving Aeris the role of primary love interest after her death, you essentially diminish the emotional weight of Tifa's arc, which is more reliant on fulfilling that role than Aeris, who also has other stuff going on.
just some ~*~*~*thoughts*~*~*~