I agree. The RAF could (relatively) easily repair and replace aircraft; you simply can't do that with large ships. The problem is though that dive bombing ships would have been extremely hazardous for the Luftwaffe. As the Japanese found when attacking the US fleet, there was a world of difference between attacking ships in harbour and out on the sea. I'm guessing that most of the German pilots would have had little to no experience of attacking packs of well defended ships, and it was only later in the war when (fairly) accurate weapons were developed.
Having said that, this was a war of attrition. As we saw in Barbarossa shortly afterwards, the Luftwaffe had an awfully large number of planes and pilots to fly them. And they had lots of factories capable of replacing their losses. It's questionable just how much damage the RN would take before withdrawing its forces. With air supremacy won, the Germans could take their time in attacking ports and harbours that the RN might have used, and with a combination of U Boats, battleships and bombers - and nothing to oppose them - the flimsy barges could cross the Channel.
The thing is though that this would have bought the army time to set up (almost) unbeatable defences. We saw in Normandy just how close the Allies came to failure - and that was with the Germans unaware of the point of attack and incredibly poor leadership back in Berlin. Imagine with months of time just how effective the British forces would be when they knew where the Germans were going to land, had dynamic commanders and were defending their home turf. Britain would have been taken eventually, but the cost would have been incredibly high.