First of all, there are different structures on a nuclear powerplant facility, some more important than others. If all they wanted to do was knock the plant offline for some time, they might target those big cooling towers. However, if they really wanted to hit a reactor with a plane, it's a lot harder. The reactor containment building is a lot smaller than a skyscrapter. It's also made of dome-shaped reinforced concrete at least 6 feet thick. The combination of thick concrete, rebar, and the curved shape makes for a very strong structure.

To give you an idea how strong the containment building is, I've seen video from a test conducted back in 1979. In the test, they took a 40,000 pound surplus F-4 fuselage and used rockets to accelerate it to 400 MPH on a test track. It hit a flat piece of simulated containment wall and only penetrated about 1 inch. The dome shaped containment of a real reactor is even stronger than that test article.