Does a US citizen traveling by plane in Mexico (international flight), for example from Mexicali to Mexico City need to have a passport?
You are asking about a Mexican domestic flight from the border zone to the interior. While it is hard to find a Mexican source that authoritatively lists domestic flight ID requirements, experience suggests that a US citizen visitor will require a passport book while US citizen residents of Mexico will likely need their resident cards.
From experience I know that Mexican residents can generally travel on domestic flights using either their passport or their resident card as ID (a Mexican driver's license may also work, but if they think you aren't Mexican they may ask for the resident card anyway). At a border zone airport, however, the airline will also be checking that foreign visitors have the FMM form they need for travel to the interior and since residents won't have one in their passport they'll likely need to produce a resident card in any case to explain why that's okay.
For US citizen visitors, while an FMM can be obtained with a passport card alone, for travel outside the border zone INM now requires they be in possession of a passport book so the airline should enforce that too. A US citizen will require a passport book to take that flight, like other foreign visitors.
What I do not know is whether alternate ID might be acceptable for a US citizen visitor flying from one border zone city to another (say, Tijuana to Juarez), but generally (allowing for the occassional unevenness of regulation enforcement in Mexico) a passport book should be required ID for all other Mexican domestic flights and the airline should be looking for FMMs as well for flights leaving the border zone.