In this question one answer states that the Soviets' Baltic fleet was stuck in the Gulf of Finland due to an anti-submarine net and mines. But the Mediterranean has plenty of narrow gulfs and straits, and yet the Allies were able to sail around doing naval invasions.
What about the Axis operations in the Gulf of Finland made it impossible for the Baltic fleet to break through?
After Soviet evacuation of Tallinn, Kronstadt became the main base of the Soviet Baltic Fleet.
The Gulf of Finland is fairly narrow and shallow in the East (where Kronstadt is located), so
...the Baltic Fleet was confined to the innermost part of the Gulf of Finland by German minefields...
Basically, the problem was that the only remaining Soviet naval base was in a spot which was relatively easy to isolate with mines, and, critically, the Germans enjoyed air superiority which enabled them to set the minefields almost unmolested.
If the Allies have placed all its Mediterranean naval forces in a "narrow gulf" and waited for the Axis to blockade them with minefields, they would have been in trouble too. However, the Allies had several bases (Gibraltar, Malta, Alexandria) which were relatively well protected from the air.
There are many reasons. Unlike Mediterranean, Baltic sea is very shallow (maximal depth of the Gulf of Finland is 115 meters, but it is more shallow in most places). So it could be completely blocked by mines. Next, the Gulf is narrow, and thus could be controlled by German aviation and artillery from the shores. Finally, unlike Britain and US, Soviet navy was extremely weak in comparison with the German navy, and it is hard to see what problems could it solve in the Baltic even if it were not blocked. It could do something only on the final stage of the war, when the Soviets occupied much of the coast, and achieved the air superiority.
