The book D-Day Through German Eyes (Holger Eckhertz) is a compilation of memoirs of troops on the German side of the Normandy landings, recorded in the 1950s. One soldier stationed on Omaha beach (a word not used by the Germans, of course, a point covered in the book) remembered 88mm PAK guns (artillery rather than machine guns) firing directly into the landing craft:

... These 88mm gunners were very accurate, and shot into the landing craft straight through the tall vertical bow. They fired high explosive, and the shells pierced the bow and exploded inside.

I saw one of the landing craft opposite my location being hit in this way. The 88mm shell detonated beyond the bow, and the bow door, which I then realised was a ramp, was thrown up into the air. Inside the craft, I could see a large number of troops who had been injured in the explosion, surrounded by men who were still able-bodied. They were clambering and scrabbling over each other, because the craft began to tip forward as water entered the open bow. I saw then from the shape of their helmets that these were Americans.

The 88mm gunners fired another shot into the mass of men, and this threw several of them directly out of the craft into the water. The whole craft began to sink from the bow, which made the stern of the craft lift into the air, and this movement tipped the men into the sea immediately. Wounded, or otherwise, they all slid down the inside of the craft as its tail rose and into the water. Such events were being repeated all along the beach, as these craft were hit or made to sink, or in some cases set on fire.

This soldier, a machine-gunner, did not fire directly into the landing craft (as happened in Saving Private Ryan) as they had been instructed to hold their fire until the enemy soldiers were 400 meters away, and this was closer in than the landing craft were able to come (at least in his zone).

His description of what happened then was nevertheless somewhat similar to Private Ryan:

The craft were stopping at a point where the water was about chest or neck height, and the men were running down the ramps and stepping into the water, holding their guns, plunging down and then bobbing up again, with the sea up to their shoulders or chests. In most cases, the men tried to advance in the water one behind the other, with each man holding or reaching for the back pack of the man in front. It was as if they were conducting a drill or an exercise.

As the last man stepped off the ramp, the craft would reverse and hoist up its bow door, and more craft would approach the beach around it. The discipline and the skill in the way the craft were handled was impressive. And so the first of these lines of men began to trudge – that is the only word I can use, they walked slowly and deliberately – they began to advance in this way into shallower water, and the waves came to their chests, then their waists. That is when we opened fire on them, as our orders stated.

... I did not sight on them individually at first, but I began firing and I swept the gun from left to right along the beach. This knocked down the first few men in each line of men; you must remember that the MG42 was so powerful that the bullets would often pass through the human body and hit whatever was behind. So it was that many of these men were hit by a bullet which had already passed through a man in front, or even two men in front. After that, I aimed more selectively, to make the ammunition last as long as possible. I fired short bursts at small groups of men and hit them that way.

... The Americans began to run, wade or stagger forwards, trying to get out of the water and onto the sand itself. They still moved quite slowly, and because of that and the close range they were easy targets to hit. In some cases, they tried to remain in the water up to their necks, perhaps hoping to be less conspicuous, and I did not fire at those men, because they showed no signs of advancing. In other cases, these troops tried to take shelter behind the anti-tank devices on the beach, which were triangles of girders sticking up from the sand. Those devices were too narrow to give any real protection, though, and those men were also hit. There were other troops who I could see removing their back packs and equipment and running onto the sand, attempting to surge up the beach towards the sea wall. I paid particular attention to these men, of course, and made sure that none of them advanced beyond a few paces.

-Henrik Naube, Unteroffizier (corporal) with the 325th Infantry Division, stationed near Vierville.

For a more technical basis for a response, it is worth noting that even if an individual man were relatively safe (not that I'd appreciate receiving the sole attention of an MG42), that's not what MGs are for in the first place. They are designed to either conduct grazing fire or to impact a beaten zone. This means that while it may or may not have been feasible to aim at an individual soldier on the landing craft ramp, they certainly could aim at the landing craft ramp in general and rely on the spread of the rounds to cause the damage to the mass of men inside.

It is also worth considering that the German MGs were dual-mode weapons. They could be rolled either as heavy machine guns or section light machine guns, basically depending on if they were mounted on a tripod or a bipod. The former, of course, being substantially more accurate, even if less common. It could be expected that a number of beach defense MGs would be the tripod mount. I'd expect that an excellent proportion of the rounds fired at, say, 400m, would impact in an area about the same as the frontal area of a small truck.