I mean, from what little I know of Russian government, that would be logical. The gov't is very top-heavy, i.e. the few in power wield significantly more power than the people do, and by power I mean combined political, economic and military power (there is no distinction between the three -- they are all components one must use in order to remain in power, for better or for worse).
It's not obvious to me if it's still on the side of democracy, or dictatorship, but it seems to be relatively stable regardless, suggesting one or the other and not somewhere inbetween. A political scientist or economist could quantify that better (well, assuming open information to base such judgement on).
Even in a western democracy, selling airspace rights would logically go to the state, at least as the primary recipient. There's no reason to believe that it should trickle down to the people, whether by offsetting overall taxes, or budgeting to some public service, or by a direct rebate. It might be logical to disburse it to land owners who are overflown by the routes (given a suitable distribution among owners, as routes are inexact, and many owners would be affected to varying degrees), but I don't think there's any basis for that in the US for example, though there may be better reasoning in others (namely, those where property rights extend up and down infinitely far).
Which is to say, I have no idea, but have no doubt that it's more or less going straight into the oligarchy's pockets (and, by extension, a majority to Putin's).
Tim