There's a few things going on here:
First, to be clear, we don't know where the island is, at least in the DCEU, but we can make some pretty good guesses and the Aegean Sea (the eastern-most part of the Mediterranean) is probably right.
If you look at the Aegean Sea on a map, it's not really that big relative to say an ocean, but it is full of islands. It's a very rocky sea, and even in the movie, we can see that Themyscira was surrounded on all sides by tons of rocky outcroppings. One of those took down the German warship that was following Steve Trevor -- it sank before it got anywhere near the island. It was only the small, very slow-moving rowboat that managed to get through the outer "barrier" intact. On top of that, the island is constantly surrounded by fog, and the fact that there even is an island there is hidden behind the invisibility barrier. Had the Germans not seen Trevor fly that way, and the one soldier not seen the glint of the downed plane under the water, it's unlikely they would have ever found the island.
In that kind of an environment, it's very unlikely that boats are going to go sailing around in what looks to be very dangerous waters. Mostly, people travelling by sea stick to well-defined routes that are know to be free of underwater hazards. And precisely because people look at the Aegean Sea as small and full of uninhabited (and dangerous) islands, there's not much incentive to explore -- everyone would just assume we knew what was there already and it wasn't worth it.
Of course, that only prevents people from finding the place by sea. Airplanes are a very new thing in Wonder Woman - the first Trans-Atlantic flight doesn't happen until a year after it ends. Planes were not nearly so reliable, and travelling out over open sea with nowhere to land, refuel, etc. isn't something most pilots would try. Trevor was desperate, trying to avoid German ground forces shooting at him, or he probably never would have flown where it did.
How, exactly, Themyscira stays hidden now is IMO a more interesting question, one that we may learn more about in future movies.