It's a liability/guilt thing. The airlines and the security authorities (particularly in Fortress USA) only want to accept your baggage if you accept full responsibility/liability for whatever may be revealed through x-raying, searching etc. So if you don't give a clean 'yes - I packed it and nobody else has so much as brushed past it since that point' response, then they regard you as suspect.
Reminds me of someone entering the USA at JFK a few years ago with his wife and young children for a holiday. He ticked 'yes' to the 'have you ever had difficulty gaining entry to the USA before?' type question. Reason being when he was a child (in the '60s) his family had visited the USA, but had some clerical error with their visa, which delayed their clearing immigration by an hour or so whilst it was rectified. This was explained in great detail to the goons at JFK, but because they couldn't verify something that far back (he should have just said nothing in the first place really), they wouldn't allow the family to clear immigration and so sent them all back to the UK on the next flight.