On the map Ebonheart Pact has the biggest territory, and it seems like daggerfall has the smallest territory though I am not sure about that.
Since you are not able to walk into enemy territories will it not be unfair that some people will have more places to explore and be in than others just because you agreed to why they should rule Cyrodiil?
Or will the territories scale until they are about equally big?

We still don't know effectively which areas will be really explorable. Just because a province looks bigger in the map it doesn't mean we will be able to go to every single place in that province, there will probably areas we can't access so they can open them in later expansions and patches. So the Ebonheart having a bigger territory really means nothing untill we see which portion of that territory is actually explorable.

Also, you can have a place that is bigger in area but with less content, so devs can compensate the smaller sizes by adding vertical areas (underground and mountains), or simply putting in more stuff for players to do in the territories that are smaller. Content and exploration possibilities does not equal the size on the map.