Commander Kidnapping refers to the use (or abuse, depending on who you listen to) of transports to "abduct" Commander units or, more generally, construction units. Transports in Spring can load enemy units as well as allied units, and enemy units become helpless once they're loaded. This doesn't often work against combat units, which can usually damage or destroy the transport before it can grab them, but can be very effective against unattended construction units or Commanders. Traditionally, airborne transports have been used for this purpose, but some mods have hovercraft transports or other kinds that can be used for similar assaults.
This is generally considered a lame tactic and other players have a bad opinion of you after that. Against a competent player,it should be impossible to pull off his com. Even if one hasn't built enough static defences, simply keeping the units the enemy's trying to kidnap moving can often prevent the transport from grabbing them. A well-managed Commander is especially difficult to kidnap, as its laser can shoot down flying transports, and its D-Gun can destroy most other kinds as they close.
Do not play with players who do that with allied commanders, period.