30 - 45 minutes isn't enough time. The best way to go (using Disney transportation) would be to take a bus to MK, then take the boat to FW. You might be able to do this in 45 minutes, but this route assumes that you are going to the early dinner show and MK is still open and the boats are still running and you don't have to wait very long for a bus or boat.
Otherwise you would have to transfer twice. Take a bus to a park, transfer to a bus going to the TTC, then transfer to a Boone or Crockett bus. Total time - more than an hour.
Getting back could be worse. When the 9:00 p.m. Hoop De Doo show is over the theme parks are usually closed, leaving Downtown Disney as the only hub. You would have to go to the TTC, transfer to a DD bus, then transfer to a BW bus. Total time - more than an hour and a half.
The real best way to go is to take a taxi. It will cost about $10 and will take about 15 minutes. Allow extra time anyway and enjoy the petting farm, pony ride and other things to see at Fort Wilderness.