At the time of the attacks, the Pentagon was under renovation and many offices were unoccupied, resulting in fewer casualties. Only 800 of 4,500 people who would have been in the area were there because of the work. Furthermore, the area hit, on the side of the Heliport facade, was the section best prepared for such an attack. The renovation there, improvements which resulted from the Oklahoma City bombing, had nearly been completed.

It was the only area of the Pentagon with a sprinkler system, and it had been reconstructed with a web of steel columns and bars to withstand bomb blasts. The steel reinforcement, bolted together to form a continuous structure through all of the Pentagon's five floors, kept that section of the building from collapsing for 30 minutes—enough time for hundreds of people to crawl out to safety. The area struck by the plane also had blast-resistant windows—2 inches (5 cm) thick and 2,500 pounds (1,100 kg) each—that stayed intact during the crash and fire. It had fire doors that opened automatically and newly built exits that allowed people to get out.

From the Wikipedia article: https://web.archive.org/web/20150622032541/http://articles.latimes.com/2001/sep/16/news/mn-46435 https://en.wikipedia.org/wiki/The_Pentagon#September_11,_2001,_attacks