The Luftwaffe seemed to be dominant in the Mediterranean in 1941 (as during the invasion of Greece and Crete), but surely it would have taken ships to land all the troops and motorized equipement of Rommel's Afrika Korps. According to Antony Beevor's The Second World War, the Royal Navy was dominant in the Eastern Mediterranean at the times of the invasion of Crete. Was it equally dominant in the Western part? If so, how did Germany managed to land in North Africa?
In February-March 1941, the RN in the Mediterranean was roughly comparable to their Italian opposition. Mediterranean Fleet had, as its main striking power, three battleships and two aircraft carriers (though for much of this period, only one was available). It could also call on Force H at Gibraltar, which had another battleship, a battlecruiser, and an aircraft carrier. In comparison, the Italians had six battleships, but three of these had been heavily damaged during the Raid on Taranto in November 1940. One, Conte di Cavour, would never be repaired, while the other two were out of action for the first half of 1941 and beyond. Mediterranean Fleet posed a considerable threat to Italian shipping, but equally, the Italian Regia Marina posed an equal threat to British shipping. This threat is part of the reason why Mediterranean Fleet did not attempt to intervene in the sea-lift of the Afrika Korps to North Africa.
While the Italians were shipping German troops to North Africa, the British were also carrying out their own troop movements. The Greeks, threatened by German troops who were beginning to arrive in Bulgaria, agreed to allow British troops in Greece proper. Under Operation Lustre, the British began moving troops from North Africa to Greece. The ships of Mediterranean Fleet were needed to cover this movement against a possible Italian strike against the troop convoys and following supply convoys. This was a real risk; the Battle of Cape Matapan, on the 28th-29th March, was a British ambush of an Italian force attempting to raid the convoy routes. With Mediterranean Fleet's heavy forces tied up protecting the convoys, a raid by lighter forces against the Italian convoys risked running into the Italian battleships and being defeated. The British also had to protect shipping elsewhere. On the 19th February, Operation MC 8 began, a convoy run to Malta. This tied up two of Mediterranean Fleet's battleships, plus the only available carrier. Throughout the period, there were frequent attempts by Axis forces to use aircraft to drop mines in the Suez Canal. This led to significant delays in shipping traffic. These traffic jams had to be protected. The delays also reduced availability of ammunition and fuel, reducing the RN's ability to make an attack on Italian shipping.
Another factor was the strength of the Luftwaffe and Regia Aeronautica. These could effectively threaten British shipping movements within the range of their aircraft. With few British airfields nearby, any move by Mediterranean Fleet would have to be covered by its aircraft carriers. Unfortunately for Mediterranean Fleet, its most modern carrier, Illustrious, was heavily damaged by German dive-bombers while escorting a convoy to Malta on the 10th January. Her replacement, Formidable, was delayed by a diversion to take part in operations against Italian East Africa, and by the aforementioned mines in the Suez Canal. She would not arrive until the 10th March, by which time most of the Afrika Korps had arrived. Without these two ships, Mediterranean Fleet had to rely on HMS Eagle. Eagle was old, small, slow and unreliable. With only her available, taking more decisive action against Italian shipping in the Central Mediterranean would be risky.
Both of these arguments apply only to Mediterranean Fleet, not to Force H. This, however, had its own duties and difficulties. The first convoy carrying German troops departed Italy on the 5th February. Force H sailed the next day, but not to intercept. Instead, it bombarded Genoa on the 9th. Force H was also responsible for protecting convoys in the Atlantic against surface raiders. With the German large cruisers Gneisenau and Scharnhorst and heavy cruiser Hipper out in early 1941, the Atlantic convoys were at significant risk. As a result, Force H spent much of February and March covering convoys and hunting raiders in the Atlantic.
While the RN's heavy forces in the Mediterranean area could not attack the Afrika Korps convoys, light forces, submarines and aircraft from Malta could still hit at them. While these did see some success, sinking two merchants and the light cruiser Armando Diaz, they were hampered by other factors. Malta was low on fuel and ammunition, and could not easily support constant sorties against Axis shipping. Comparatively few submarines were available, and the light forces were needed to protect the heavier units in the work outlined above. The Italians had laid large minefields to protect their convoy routes. These mine barrages posed a significant threat to any surface raid or submarine attack. The convoy routes were also only briefly exposed to attack. The most dangerous part of the crossing, from the tip of Sicily to the Tunisian coast, could be done in well under a day's steaming, even for a slow merchant. The Italians stuck close to the Tunisian coast, making it harder for subs to engage them and taking them further from British aircraft on Malta.