A few of my previous posts have answered questions about the air war on the Eastern Front:
Why the German's didn't firebomb Stalingrad
[The evolution of Soviet fighter design during the interwar years and the beginning of WW2] (http://www.reddit.com/r/AskHistorians/comments/1sxlgt/what_were_the_main_national_differences_in/)
A few basic points to take away are:
The German Luftwaffe was a serious force to be reckoned with at the onset of Operation Barbarossa. In comparison, the Soviet Air Force consisted of antiquated planes that suffered from lack of proper maintenance and poorly trained pilots that were quick to run away from their Luftwaffe counterparts.
Lack of a central command system or tactical battle plan for the Soviet Air Force. While the Luftwaffe was used as ground support, tactical bombing, and fighter combat patrols, the Soviets lacked a consistent battle plan during the first years of Barbarossa. This allowed the Luftwaffe to gain a significant air superiority from the outset.