Several points please. In France 1940 most of the Luftwaffe losses were from ground fire, and operational loses. The Spitfire I/II could hold it's own against the Bf-109E. It could turn faster in most cases, and was probably a few MPH faster in level flight at most altitudes. The 109E could out climb, and dive the Spitfire, and had superior performance at high altitudes. The F model was superior in all but tight turns. The Spitfire V was a significant improvement over the I/II, but was still out preformed by the Fredrick in most measures, especially at high altitude, which wasn't that relevant in North Africa, where most fighting was at low-medium altitude. The F model was far superior to the P-40's, and Hurricane II's it faced at that time. The air to air loses at this time were nowhere near close. German Experts were raking up amazing scores at this time, but were making the mistake of slaughtering escorting fighters, and letting the bombers get through. The F wasn't as good a bomber killer as the E, or later G versions.Simply because the Bf109F was superior to the Hawker Hurricane II and the Curtiss Tomahawk, doesn't give the Luftwaffe a free pass to fly unmolested from Crete to North Africa. During the invasion of France and the Low Countries in 1940, the Bf109E was definitely top of the food chain. It was simply better than the Hurricane I, Dewotine 520, MS406, Curtiss P-36, Fokker D.XXI, and any other fighter the Allies employed until the arrival of the first Spitfires over Dunkirk. Nonetheless, the Lufwaffe managed to lose 1,129 aircraft to enemy action (source Frieser, Karl-Heinz (1995). Blitzkrieg-Legende: Der Westfeldzug 1940 ).
The notion that the Tante Jus flying in from Crete would have an effective close escort of 109s also needs closer examination. The lesson from the Battle of Britain clearly show the that Bf109 was not well suited as an escort fighter. Let us look at the details of the proposed operation.
The distance from Heraklion to Gambut is around 250 miles one way, as the crow flies. Sources differ, but in general the Bf109 F had a cruising speed of around 310 mph and a cruising range of around 520 miles with a 300 litre drop tank. Superficially, this looks like a simple assignment.
However, the Ju 52s were considerable slower. They had a cruising speed of 153 mph and an economical cruising speed of 130mph. Given that they would be carrying as much as possible, it would be fair to go with the lower figure. So, it's a minimum two hour flight, with perfect navigation, no headwind and no enemy interference. The 109s would either have to throttle back and fly at a very uneconomical speed to stay close to their charges, or to weave pretty patterns above and around them, all the way to Gambut and then all the way back with the empties. Not only would they burn more fuel in either scenario, but they would also be exposing the Ju52s to attack. They would either be too close and too slow to be able to react, or they would have to react to an attack that was already underway. Given the extremely poor combat effectiveness of the Junkers 52, even a single coordinated gunnery pass against them will undoubtedly cause heavy losses. This was proven every time they were used in contested air space in daylight – including the OTL resupply runs across the Med.
In addition, any weakening of Luftwaffe units in Sicily to provide escorts for supply runs from Crete would undoubtedly ease the passage of the Operation Harpoon convoy to Malta between 12th and 15th June. This would further hamper any Axis resupply missions across the Strait of Sicily.
Given the need for the Luftwaffe to continue to dispute air supremacy over several battlefields at once (in just this theatre), it is far more likely that the Luftwaffe would assign Bf 110s as escorts. They had a far longer range and were much less in demand over the battlefront than the hard worked Bf109Fs. Of course having seen the 110s performance during the Battle of Britain, these aircraft would find it much more of a challenge to try to dogfight with Hurricanes and P-40s.
Probably more crucial than anything mentioned above, there is also the question of the availability of Ju 52s. From 20th February 1942 Ju 52s were withdrawn from all other theatres (including training machines from Germany itself) to fly in supplies for troops encricled in the Demjanks and Cholm pockets. Although they had to fly 160km over Soviet control territory, around 600 Junkers 52s succeeded in flying in around 305 tons of supplies per day. A fairly impressive achievement. However, they only face limited resistance from the Soviet air force, which was still weakened from the initial attacks of June 1941. Even with this limited air defence, the Luftwaffe still lost almost 300 Ju 52s in an operation which lasted until 18th May. (source Pimlott, John, 1998, Die Luftwaffe, Neuer Kaiser Verlag).
To then immediately reassign the surviving aircraft to the Mediterranean theatre for a similar resupply operation, over greater distances and with more effective opposition is an unlikely recipe for success. The aircraft needed maintenance, the crews needed rest, and the multi engined flying schools in Germany needed their surviving instructor pilots and planes back.
So, to summarise, resupply flights from Crete would not be an easy undertaking.
The Axis frequently used bombers for transports, and in addition they could tow some of the gliders for Operation Hercules to move men, and small arms. Their not trying to fly in heavy equipment, mostly men, with small arms, and personal kit, to serve as replacements. Gliders with their landing gear in place can be towed out, and reused, since their landing at airfields, not making combat landing in open fields. One squadron, (staffel) of Bf-109F's would be enough for escort duty, using the weaving method to keep their speed up. They don't have to do round trips, they land to refuel with their charges, and fly back with them.
Since the Desert Air Force would be forced back to airfields in Egypt what would make you think sending fighters over the sea to look for troop transports would be a priority? Most of their fighters would be busy escorting their own bombers, and trying to give cover to their own ground troops. Again since the Axis did fly in reinforcements in the OTL why is it so far fetched that they could do it in this TL? Since cardcarrier is only talking about moving 4,000 men, were only talking about 200 bomber sorties, or less over several days.