2012

Doesn't flying over an earthquake in an airplane make it so that the passengers feel an earthquake flying over it?

Because if so then something was dead wrong in 2012.

Not in particular, no.  The ground during an earthquake is generally not moving enough to significantly disturb the air above it, thus there would be negligible effect to the aircraft.

However, if anything results in a large amount of debris being shot into the air, such as an earthquake caused by a volcanic eruption or a particularly pissed-off tornado, the aircraft would be affected by this.