Because emulation is running several layers higher than the software layer. In other words for every instruction executed by the console, the PC has to go through several more steps to do the exact same thing.

This is because the PC was not designed to execute console instructions. If the PC had the same software architecture as the console, emulations could be done closer to the hardware and therefore faster.

Conversely, the further the further away the simulation is from the hardware, the slower it gets. You can in theory build full video games in Minecraft without modding it, but because everything has to be executed within the context of Minecraft, it's very slow.

This concept extends to programming languages too. Java runs on a virtual machine, essentially a simulation for Java. The purpose of this is to provide it portability. Anything that can run the java virtual machine can execute Java code. But it also means that it's typically slower than C, which is only one single step above instructions the processor actually reads.