Sure, Bakiyev went to Moscow and picked up a couple of billion dollars to close the U.S. airbase, but one can see how the decision was made easier. From the Associated Press:
The Manas base is the only U.S. toehold in strategic Central Asia, lessening U.S. bargaining power.
American officials will admit, in private, that they made their hold on Manas more vulnerable to Russian and Kyrgyz government pressure by mishandling a number of incidents at the base in recent years. The first was the fatal shooting in 2006 by a U.S. serviceman of a local civilian driver at an entrance to the air base; the U.S. investigation dragged on and Washington refused to allow the Kyrgyz to prosecute the American.
Also in 2006 a U.S. Air Force KC-135 refueling plane collided on the runway at Manas with a Tu-154 aircraft carrying a senior Kyrgyz government official, slicing off a portion of the civilian plane’s wing. The Americans blamed the local airport control tower; the Kyrgyz authorities said the U.S. pilot was to blame.