Can you conquer 3 cities with the flight card?
Yes, an attacker can conquer 3 cities with the Flight card as long as all three rival cities are within 5 spaces of one or more of the attacking player's friendly spaces at the start of his turn. (That is, an attacker cannot target spaces that have come within range due to spaces just conquered that turn.)

Based on your description, it seems you are playing by the correct rules, although the terminology is being confused. "Masonry" is the first level Military cards. The Industry cards are responsible for building cities (e.g., "Pottery", the first-level Industry card).

Strategy-wise, if you're finding Flight (the fourth and most powerful Military card) to be overpowered in your games, here are some suggestions:


Cut back on building cities on low-numbered terrain as it makes them easy targets for attacks (the exact symptom you're experiencing)
Make use of reinforced control tokens as they can greatly enhance the defense of surrounding friendly spaces. (Each adjacent reinforced control token adds +1 to its neighboring friendly space's defense.)
Allocate and stockpile trade tokens on the Military card to discourage would-be attackers.