Although the United States has signed (last July) an agreement with Russia that allows 4,500 air transports a year to cross Russian territory on their way to Afghanistan, the route is only being used at the rate of about 700 flights a year. Why isn't the full capacity being used? Partly because of a squabble among Russian bureaucrats. Although the agreement waived transit fees, Russian aviation officials insisted some kind of fee had to be paid. It took months to sort that out. And there are still issues with some Russian ministries over how the flights should proceed.
But there are other elements at play. The U.S. already sends huge amounts of cargo through Russia via railroad, which has been very lucrative for the Russian railroads. Many of these trains go to Manas airbase in Kyrghyzstan, where many of these flights through Russia land as well. Manas is mainly a base for aerial tankers (that refuel about 30 aircraft a day over Afghanistan) and a staging area for supplies that are brought through Russia by railroad, then flown into Afghanistan from Manas. For the aerial tankers, their fuel and other supplies also come in via rail. While flying through Russia is cheaper than coming in through Pakistan (via the Persian Gulf and Indian Ocean), railroad is more than ten times cheaper than any air route.
Most of the through flights via Russia are carrying military personnel (50,000 or more a month), and these were suspended for over a week because of the current revolution in Kyrghyzstan. But the aerial tanker flights, which account for most of the activity at Manas, continued. Russia apparently backed the Kyrgyz rebels, in another attempt to get the Americans expelled from the base at Manas. But the Kyrgyz rebels aren't stupid, and know how to get paid by both Russia and the United States.