In World War 2, why did the Allies land on the beaches that were heavily fortified with pillboxes and machine gunners and whatnot? Surely there were some beaches in Europe that were not being defended by the Germans.

Here, I'm going to assume you're talking about the Normandy landings. The beaches of Normandy were selected because they were the best option out of all the sites that were considered, and presented the highest probability of success, and minimized the risk of defeat. Even though the Normandy beaches were defended with machine guns and artillery, they were the best choice given the distance from England, the Allies' naval capabilities, and their wish to gain a quick victory with as few unnecessary losses and avoidable military mistakes as possible.

Four sites were initially selected; the Pas de Calais, Brittany, Normandy, and the Cotentin. As Brittany and the Cotentin are narrow peninsulas (especially the Cotentin), it would be quite easy for the Germans to rush up troops to cut off the neck of the isthmus after the Allies had landed, trapping them and leaving them nowhere to go but back into the sea. For that reason, these two sites were rejected. The Pas de Calais seemed like a logical landing spot, as it is the closest land on continental Europe to the United Kingdom (large German coastal guns were able to fire at the United Kingdom across the English Channel at this point!) Because of this, it was heavily fortified as part of the Atlantic Wall, more so than the most heavily defended parts of Normandy. The Pas de Calais was bounded beyond the beaches inland by many rivers and canals that allowed the Germans to set up defensive positions and would make Allied movements constricted (hence predictable) and difficult due to the perils of battlefield river crossings (see the disastrous attack on the Rapido River in Italy, January 1944) With these other choices eliminated because of tactical and strategic reasons, that left only Normandy. If Brittany or the Cotentin was attacked, the German high command would know right away the Allies' first route of advance (out of the peninsulas) and could cut them off and destroy them while committing less of their troops, than if we landed on a broad front.

Before the landing, the inland rail network of Normandy was cut by the French Resistance in over 500 places, isolating it from the rest of France and making it difficult for the Germans to move reinforcements around to meet an Allied attack, Cutting the rail network throughout the land mass of a peninsula doesn't really accomplish anything except delay your own troops' advance out of it; the Germans could just sit at the unmolested neck of the peninsula and blockade it, still being able to move troops freely in and out of the line.

An assault at Normandy could go in multiple directions; it could simultaneously threaten the Germans' port facilities at Cherbourg since Normandy was poor port territory (not to worry, we essentially brought our own port with us) or enable a lightning thrust south, or south and then east towards Paris and the German border. This uncertainty would throw off and complicate the Germans' defense strategy. If the Allies landed at Normandy, the Germans would not initially know which way we would go; a turn northwest towards Cherbourg (which actually was the first move), an attack south to expand the beachhead (the second move), or an attack to the southeast, towards Paris (the third move)

Remember that many of the small landing craft the Allies used had relatively poor seagoing characteristics when loaded, or traveling on the open sea during storms. Their range was also sometimes very limited. This resulted in them being carried on davits, or split into sections and carried on the decks of larger, seagoing ships; the sections were then lowered by crane into the water and reassembled. The shorter the distance these small craft had to travel, the better.

Sources:

Overlord: The D-Day Landings, by Ken Ford and Steven J. Zaloga

D-Day: The Battle for Normandy, by Antony Beevor

D-Day, June 6, 1944: The Climactic Battle of World War II, by Steven E. Ambrose

The Day of Battle: The War in Sicily and Italy 1943-44, by Rick Atkinson

A Study of Rear Area Security Measures, Special Operations Research Office, Counter-insurgency Information Analysis Center, United States Army (1965)