Lexington Institute issue paper - Why do the Alumni Get The Pentagon's Plum Jobs? By Loren B. Thompson.

There was a time when the assignment of top jobs in the joint force resembled the workings of the congressional seniority system more than a merit-based selection process. Representatives from each of the three military departments were awarded a roughly equal number of positions, with certain commands seemingly reserved for a particular service. That system is now gone, replaced by a joint command structure in which Navy Department alumni get most of the plum jobs. The Bush Administration plans to replace the Marine general and Navy admiral who currently head the joint staff with two more sea-service representatives. Admirals are running Central Command and Southern Command, while retaining their lock on Pacific Command.

Such a lopsided preference for one military department would have been unthinkable in the Clinton years, leading to bureaucratic warfare in the Pentagon and on Capitol Hill. But looking at the apportionment of senior military positions under Bush, it's as though the Navy and Marines had become separate departments, while the Army and Air Force had reunified after 60 years of separation. What does this "sea change" mean? Is it a reflection of passing circumstances, such as the Army's preoccupation with Iraq, or a more durable pattern? An examination of forces driving the change suggests that the rising tide of Navy leaders is unlikely to recede anytime soon...
More at the link to include some possible reasons...