You are comparing a system simulator to an instruction set simulator. Those are very different things.
When you run an application on QEMU on Linux, only the application code is simulated (by just-in-time compiling every basic block when it is first executed, then always just executing that compiled native code). System calls go to the Linux kernel on the host system, which runs as usual. Hardware is not virtualized. In contrast, Virtual PC (if I understand correctly) simulates the hardware of an entire PC, including graphics hardware, and runs all of Windows on top of that. That's a lot more expensive in terms of processing power.
That said, sure, you will probably lose some performance with QEMU. If the simulated code uses lots of fancy vector instructions that are not provided by the host hardware, you'll even lose a lot.