Erosion, water and the atmosphere. The atmosphere protects the surface from some impacts, causing a larger number of small sized impactors to blow up in the air before reaching the surface and forming a crater. A similar effect happens with smaller impactors that hit the ocean and aren't large enough to make a crater in the ocean floor. The big factor though is erosion and plate tectonics. If you look at the surface of Mars most of that crust is ancient, billions of years old. On Earth the crust gets recycled constantly due to tectonics and volcanism. The big island of Hawai'i is a fraction of a million years old, for example, and the ocean floor keeps getting recycled in a process that keeps most of it under 150 million years old.

Then you have erosional processes due to the air, the water cycle, life, etc. Mountains get worn down, surface features get changed by rivers and shorelines, rocks get changed and moved around, life covers up or erodes surface features, etc. There's a huge crater in the Yucatan peninsula from the impactor that ended the reign of the dinosaurs 66 million years ago, but it's not easily visible to the naked eye because of all the erosional processes that have occurred since then. Remnants of older craters have been found but they are also not easily visible because of erosion. Smaller craters have a tendency to get completely erased by geological activity and erosion.