To allow for fixes in the field. You can't really repair hardware once it is shipped, but you can reprogram an FPGA to fix a problem in a bunch of logic so it is better to have that logic in an FPGA than to have it hardwired.
Don't be surprised if an upgrade to your OS also reprograms that FPGA.
I'm not sure about the FPGAs the parent comment is specifically talking about, but often FPGAs in general purpose devices are used just for glue logic - that is, buffering and interfacing between different types of busses.
