yes but only to places you have been to already,and you cant fastravel from the subways,or when there are enemy's nearby.
This problem is similar to Oblivion. I remember people wanting to be able to fly into the Imperial city when the flying wings mods came out and there wasn't anything in the Imperial city because the game is also cell based. Cells are like hyperlinks that take the player to a new enviroment within the game. Obviously adding flying to Fallout 3 will have some problems, but if the SDK gets released then anything is possible.