Arduino is not a PC but an embedded processor, it has no operating system that shields of the low level thingies (HAL)
When you program an Arduino (or similar device) youare have to programming much closer to the hardware level than you typically do in an PC environment where every device is e.g. a (more or less) nice .NET Class.
If you take a few days to go through the tutorial section, and study, execute, adapt the sketches there you will see most register and bit-masking thingies is not very very difficult. But it takes several dozen projects to get used to it.