"Best thing I've seen at BAA Heathrow was a pilot having a the knife from a set of cutlery in his flight bag removed at security - he was allowed to keep the fork. Don't really think the Captain would need cutlery should he want to bring down the aircraft he was in command of..."
While some of the items confiscated do seem daft, the arguments often presented that pilots can harm their plane anyway don't work.
If pilots weren't searched they could be used to carry weapons or bombs through security. These could then be given to passengers on other flights. So if passengers can't have an item for security reasons, pilots can't have it either.
It may sound implausible, but it is incidents at the 1 in 10 million level that people are trying to prevent.