Most of the shipping that would be lost were commondered shipping so the loss to the navy would be marginal. The bulk of the naval power was 'yet to be built' Uboats and other coastal craft like Mboots/Sboots/RBoots/KFK etc .
So loss of the surface fleet would have marginal impact since it had only marginal impact anyway. Loss of prestige for Hitler would weaken him and force him to reconsider his options in the east, since acting in 1941 was motivated to indirectly isolate the UK. The loss of Naval & air armaments plus man power would be offset by similar losses on UK side. It might have the effect of creating a 'stalingrad' level seachange in Hitlers thinking... and put him at risk of being over thrown.
The loss to the Kriegsmarine would be marginal, but the loss to the German economy wouldn't. Germany would be hard-pressed to replace those barges in wartime. We're talking a 30-40% loss in traffic along the Rhine and other inland rivers. That, coupled with a loss of material, is going to set Germany's wartime economy back enormously. On equipment and industrial loss alone, we'd likely see Barbarossa delayed until 1942, unless Hitler does his typical "press ahead at all costs" maneuver, which isn't out of the question.
As butterflies, you might see a potential expanding of Free French forces. The problem with this (if we imagine a mid/late-July Sealion attempt) is that the British shelling of the French fleet at Oran is less than a month gone. Any increase in French interest is going to be more than set off by the Oran Incident. You could see the French African colonies joining de Gaulle sooner (in OTL, they joined in autumn) but beyond that, there's not many allies to inspire towards victory.
And indeed, if the failed invasion is bloody enough, it may have a counter-effect from what we all think likely. If a Britain, having barely survived a German invasion (even if they just think that they barely survived), sits alone facing the rest of the German army, with no allies in Europe, Britons could ask themselves if it's all worth it. Given the "fight on" spirit we saw in OTL, I don't think it's likely, but I'd like to throw that out there as an option.
As to the course of history, I honestly don't think we'll see massive changes down the road. Japan will still bomb Pearl Harbor, bringing the United States into the war on the side of the Allies. Germany will still invade the Soviet Union (in 1942, if not 1941), and the Allies will still win by grinding the Axis down with superior logistics and nuclear weapons.
In the short run, I could see Hitler not wanting to send the Afrika Korps to help Italy. This would be somewhat countered by the loss of British soldiers who in OTL were deployed in Africa in the Battle for Britain. But there will still likely be a coup d'etat against Yugoslavia's pro-Axis Prince Paul, forcing the Germans to intervene just as in OTL. They'll then get drawn into a Balkan-Greco campaign, just as in OTL, but with no Cretan invasion.
Hitler would likely follow the same pattern that he did following the immense loss of paratroopers in OTL's Battle of Crete. In OTL, he never again used large numbers of paratroopers en masse via air drop. After being burned in Sealion, he'd never again commit the Wehrmacht to a location not accessible by land. But because of the Sealion losses, Hitler now has a full year to regroup before Barbarossa. That's a good thing for the Soviets, who will be far more ready for the German invasion, when it comes. Perhaps Stalin will even take the warnings seriously this time, and meet force with force.
By 1943, with Germany bogged down in Belorussia, the Allies are ready to launch operation Sledgehammer, and push forces ashore in France. The drive across France is successful, and after a winter of fighting along the Rhine, the Allies advance into Germany. Soviet and Allied forces meet along the Elbe, and Germany surrenders on June 6, 1944.