When we entered the Stans after the fall of the Soviet system, we were welcome because we offered a link to the outside world, and some assurance that by this connection the former soviet states wouldn't be reabsorbed.
That was then. These regimes still don't want to be reabsorbed by Russia, but they also don't want to give up power. Faced with a choice of democracy with them out of power, or aligning themselves with a weak and distant Moscow, its an easy choice.
And with China vying for attention, the Stans have another alternative power center to look to if they need to counterbalance the Russians. They aren't without alternatives as they were in the early to mid-nineties.
I'm not sure what tools we have at our disposal. I think our choice is to remember that we are there at Russia's and the 'Stan's invitation. We can keep our focus on counter-terror, or we will be pushed out.