Correct me if I am wrong. But you could not use protected against damage from the Gamma bomb, The Bomb is not an attack, so I ruled today that protected could not be used. Was I correct in my assumption?

Protected from the players guide.

Choose a character.

(Optional) If the character does not already have two action tokens on it, damage dealt to the character as a result of a single attack is ignored. After that action is resolved, give the character an action token and remove this feat from the game. If the character already had one action token on it, giving it a second action token deals pushing damage normally.

Immobile. The Gamma Bomb can't be destroyed and begins on the green starting line. At the beginning of each player's turn, if it's not disarmed, click the dial once to the right. Once per game per character, a character occupying this square can be given a free action to roll a d6. On a result of 4 or 5, click the dial 4 clicks to the left (12 is the maximum), and on a result of 6, disarm it. When the red line is crossed, deal 3 damage to each character and destroy each object, wall, and square of blocking terrain within 8 squares and then remove this object from the map.

You ruled correctly. Damage from the Bomb is not from an attack, and therefore Protected could not be used to negate said Damage.