The first reason, pay hikes and step increases, is business as usual and is unlikely to have explained this change.
The National Security Pay Scale could easily be a big contributor, as could easing pay caps.
The federal government competes for talent with the private sector, and tends to pay quite a bit lower than the private sector would for similar positions. Here is some information about ongoing efforts to address the fact that federal employees are generally paid less than non-federal employees doing the same levels of work in the same localities.
“When uniformly applied to GS employees [federal employees paid on the General Schedule]within a locality, the adjustment is intended to make their pay rates substantially equal, in the aggregate, to those of nonfederal workers for the same levels of work in the same locality.”
“FEPCA also stipulates that a certain percentage of the target gap between GS average salaries and nonfederal average salaries in each pay area is to be closed each year. Twenty percent of the gap was closed in 1994, the first year of locality pay, as authorized by FEPCA. An additional 10% of the gap was to be closed each year thereafter, meaning that 30% of the gap was to be closed in 1995, 40% in 1996, 50% in 1997, 60% in 1998, 70% in 1999, 80% in 2000, and 90% in 2001. By January 2002, and continuing each year thereafter, FEPCA specified that amounts payable could not be less than the full amount necessary to reduce the pay disparity of the target gap to 5%. In each of the years since 1994, the locality pay increase has been implemented at a much lower percentage than the law requires. As a result, the gap is being reduced slowly; 23.5% of the gap was closed in 1995, 25.9% in 1996, 28.3% in 1997, 29.2% in 1998, 31% in 1999, 33.5% in 2000, 38.1% in 2001, 42.3% in 2002, 44% in 2003, 53.7% in 2004, and 58.84% in 2005.16 These percentages represent the gap as recalculated after each adjustment.”
From here, and there’s lots more detail: http://digital.library.unt.edu/govdocs/crs/permalink/meta-crs-7938:1
It talks a little about the changes that may have resulted in the increases observed in the USA Today article when they were still in the proposal stage. The federal government is competing for people who could make a lot more running transportation and security/ defense related operations in the private sector, primarily in high-cost areas like Washington, DC. The recent changes have created the flexibility for the federal government to pay salaries closer to what the private sector pays in fields that have high demand.