I prefer having some form of fast travel in my games - now that I have a wife, a kid, and a full time job I just don't have time to spend an entire gaming session just walking from point A to point B. The first time out is one thing, but you can only travel between two fully-explored areas so many times before I start to find it redundant.
I much prefer game designs where fast travel is free and provided for you no-muss, but where there are definite incentive for trekking on foot. I still think Red Dead Redemption hit the nail on the head with this one:
Firstly, that game provided you with the option to fast travel anywhere at all so long as you could find a flat space to "set up camp." On top of that, there were two other methods of fast traveling by either carriage or train. The nice thing I liked about those modes of transportation was that you could "warp" to your destination at will, or also just sit back and enjoy the sights as the journey was made in real time (often with various camera angles to choose from.)
And of course having a horse helped to bridge the distance between areas.
But I think just as important as all of that was how the game design encouraged physically walking (or riding) between places. You had random encounters that would pop up, and tons of collectible missions where it tended to be more efficient to find those flowers and hunt those animals while you were on the way to somewhere else. I found in that game I very rarely made use of fast travel - there was just always some incentive to travel in-game.
I really think the "answer" to the age-old fast travel debate is to make sure you're not punishing players for using that mechanic (I don't think there's any need to restrict free-form fast-travel or charge resources to make use of it,) and more to focus on giving players ample incentive not to use fast travel.