First of all your premisse is not correct. There are several examples where amphibious landings were repelled. But i see where you are coming from.

I interpret your question as: "Why were most these landings so successful when they look so difficult on paper"

Its important to note that the attacker defines the parameters of the battle. He chooses to attack and therefore has created the neccessary conditions for his attack. This is especially true for attacks which have huge consequences if they fail. If an operation decides over victory or defeat you think twice and make sure to gather enough ressources. If a belligerent is not desperate he will obviously choose his battles wisely. This becomes more relevant the bigger the battle is.

Example Normandy:

The allied had no real pressure, obviously they wanted to end the war and free the ocupied countries but they had no real pressure like the Germans when they planned Zitadelle for example. Knowing this they had enough time to prepare properly and gather ressources. Since the allied had the luxus to pretty much have "infinite" ressources they just used enough troops, material to "assure" success. At some point you can just force victories. Since the normandy landings were important they would use enough ressources to be prepared for "everything".

Amphibious landings have big consequences if they fail so normally you will find that the attackers use material lavishly. Keep in mind that most of these big landings were done by western allied which had a lot of ressources to their disposal.

In short: A failed big amphibious landing has huge negative consequences therefore the attacker will concentrate more material to prepare for most possibilities. Amphibious landings were often done by western allies who had a lot of ressources and had the time on their side.

Without going into detail the Dieppe Raid could be considered a disastrous amphibious landing. You should check it out.

Something i think needs to be said: There is often the misconception that the attacker has some form of disadvantage this is not true. Many many people seem to believe this. But in general this wasn't true for World War II. The attackers defines the parameters of the battle and then chooses the "weakest" spots in the enemy defense. Furthermore he pretty much always has the numerical advantage since he concentrates his forces and enemy is spread thin since he tries to defend the entire front. If an attack without desperation, planned by good generals with ressources at their disposal, is conducted you should expect a victory.