Looks to me as if the guy who had the car before you fitted a Motorola phone kit and didn't want to mount an antenna on either the roof or the inside of the windscreen, so ran it to under the bonnet to get a better signal - not sure why you would do that as it is much simpler to fit a glassmount strip on the inside - I've actually got one built into my tax disc holder. I assume he uninstalled the phone kit when selling the car, but couldn't be bothered removing the antenna.
Can't think what else it could be. Have you tried chasing the wire back to wherever the other end is?