It's not a security issue it's a airline "power" play. They can control how they price and ticket your fare. If you don't get on at leg 1 the entire reservation is dropped from the system.
The discount prices are created to generate business. Since most people want to fly at the most convenient times the airlines will lower fares for very early or very late flights to fill those seats.
They might also create a lower fare to funnel passengers to their hub cities (i.e. Delta to Atlanta).
If someone wants to accept the inconvenience of spending the night in Atlanta then they can get the fare. Actually with the local hotels providing shuttles to and from the airport it's not a bad way to go.
Some links to read in your spare time:
January 15, 2005 - A Change in the Way Airfares Are Calculated:
http://www.acte.org/resources/press_rel ... 1205.shtml
Up and Down Airfares
http://budgettravel.about.com/cs/airlin ... rfares.htm
Travel Library FAQs
http://www.travel-library.com/rtw/html/faq.html
Budget Basics 101 - Airfare Deals
http://budgettravel.about.com/cs/airlin ... rfares.htm