Heather Berkman writes in Foreign Policy that it's mostly about drug interdiction. Plus there's no place much better in Central America for a U.S. president to visit:
"… El Salvador has remained politically stable. Honduras is still regrouping following the ouster of President Manuel Zelaya in 2009. Guatemala's government lacks the resources and the political will to effectively combat drug traffickers. Throw in the likely reelection of Daniel Ortega in Nicaragua this year, Washington's ongoing tensions with Panama's mercurial President Ricardo Martinelli, and Costa Rica's lack of regional political weight, and El Salvador begins to look more like Washington's foothold in the region."
Entering El Salvador overland from Guatemala, bananas welcomed us to this republic.