The problem is that flash memories have a limited number of write cycle. Depending on brand and technology, you can usually write a single flash cell between about 1000 and 100000 times. In a PC-memory configuration, this means that your memory will die in a fraction of a second.
What you could do, and that is what a typical embedded device has, is to program the memory footprint of the executable code in the flash. That way it will run instantly. The memory organisation of the PC is not meant for this kind of use however, so you have to program everything yourself, including the OS (or perhaps you could use some RTOS for i386).