Looking through the books a bit at the numbers for June 6th alone.
8th Air Force dispatched:
-4792 aircraft that day fighters and bombers in support of the invasion
9th Air Force dispatched:
-1662 transports and 512 gliders
-3342 bombers and fighters
Total being 5516
So just the USAAF put up over 10,000 sorties that day.
Not all were 'effective' sorties, but they were aircraft that started out on the mission. Losses could have occurred with any of the planes. Throw in the RAF numbers and all of a sudden losing 4000 aircraft over the course of 3 months doesn't seem all that much and I'd imagine when weighted against the total sorties flown is a small percentage.
Just found a number of total Allied Sorties flown on D-Day of 14,674 with 113 aircraft lost, many to friendly fire. Luftwaffe put up 319 Sorties.
That's just numbers and not considering the horrible loss of life to those aircrew BTW. We did the track from Caen to Falaise in the summer of 2005 and the cemeteries are full of fighter bomber pilots alongside the ground troops

The John Foreman book I've referenced "1944-Over the Beaches"
http://www.abebooks.com/servlet/BookDetailsPL?bi=9524108658&searchurl=an%3DJohn%2BForeman%26kn%3D1944%26sts%3Dt