Patrick Barry at Democracy Arsenal provides an excellent explanation of the cognitive dissonance resulting from the combination of:
a) what is widely recognized as Russia's role in prodding Kyrgyzstan to close Manas Air Base
b) Russia's decision to allow the US to ship supplies for the war in Afghanistan through their territory
Barry argues that these two seemingly contradictory actions by Putin and pals should be viewed through the prism of conflicting Kremlin priorities--and possibly internal squabbling.
On the one hand, given its problems with separatism and considerable Muslim population (and probably given its history with Afghanistan), Russia would probably like to see the Taliban and Islamic extremists in general go down in flames in the region. But, on the other hand, American entree into Russian "Near Abroad" states like Kyrgyzstan, Uzbekistan, and Tajikistan (all of which are, according to the Kazakh national anthem, run by little girls) in support of operations in Afghanistan is seen as a threat to Russian hegemony in Central Asia. Pushing for the closure of the Kyrgyz base while permitting transit of American supplies through Russian territory allows Russia to flex its muscles in what it considers it sphere of influence while simultaneously aiding the US in its fight with the Taliban.
This is really a neat encapsulation of the current US-Russian relationship: extremely at odds on some issues but quite compatible on others. Eventually, Russia may be forced to make a decision on whether fighting extremism or playing the new Great Game v.2.0 is ultimately a higher priority.