This map shows the paths taken by the various flotillas involved in the landings. As you can see, they were drawn from ports all across southern England, not concentrated in a single location. But, you might ask, couldn't a reconnaissance plane have spotted the ships as they left port and sailed across the Channel? Even if they had, it wouldn't have done much good- the first airborne forces were landing as the ships got under way, making a surprise rather difficult at that point.

We must also consider the relative state of the Luftwaffe as compared to the USAAF and RAF. In 1944, German aircraft were being destroyed (and to a lesser degree, replaced) at an astounding rate. This was due to several factors- air action in the east and Allied bombing of bases and production facilities were two of the big ones, but a less obvious cause was also critically important. When the bomber formations were flying over Germany and occupied territories, German fighters would engage them, and consequentially also engage their fighter escorts, P-51s and others, leading to great numbers of losses on both sides. The Allies used this to their advantage in a campaign known as Big Week- massive attacks on German aircraft production with heavy fighter support, in order to harm the Luftwaffe both immediately and over the coming months.

The net effect of all this was an enormous drain on Luftwaffe materiel and manpower- through the five months of 1944 leading up to the Normandy landings, over 2,200 German fighter pilots died. That figure is roughly equal to the number of German fighter pilots at any one time- a 100% casualty rate in five months. Now, these losses were being replaced, for the most part, and of course many of the veterans would survive this period while the new recruits were being gunned down, but the quality of pilot training was rapidly deteriorating to keep up with the attrition, and the aircraft industry could not keep pace. At the same time, the Allied air forces (especially American) were ballooning in size. This imbalance gave the allies near-total air superiority over Britain's airspace and much of Western Europe, meaning that they could both heavily bomb targets in France and protect their own forces from aerial attack or observation, for the most part. A useful numerical comparison- less than a hundred German sorties were flown to contest the landings, while the Allies had over two thousand bombers alone supporting the attack, each of which could fly multiple sorties over the course of the day, and that's to say nothing of all other types of aircraft involved. Faced with that kind of overwhelming force, the idea of a lightly-armed reconnaissance aircraft flying over England in broad daylight is ridiculous.

TL;DR: Many of the pilots were dead, most of the ones who weren't had been pulled back to protect the German heartland, and if anyone remaining was stupid enough to try it, they'd be shot down too.