Alright: The shields on a ship have to be incredibly strong. Why? These things engage in combat against many vessels. The Executor was designed to face off against more than one vessel. Also, I don't know if you know this or not but a Proton Torpedo IS a nuclear warhead. (Source: Ultimate Cross-Sections: Star Wars Original Trilogy) The executor is not stopped by one, it is stopped by MANY at the SAME time in the SAME position. Read X-Wing: Bacta War for a good description of how the Lusyanka (Sp?) was defeated and then remember that it surrendered to prevent total destruction and there were tons of other factors at work.
Short Answer: Learn Star Wars more, Executor is the most powerful ship in the galaxy (Exception: Death Star) in its time frame, period.