I feel it depends highly on the size of the game world - some games half the fun is in the journey, Red Dead Redemption comes to mind as a place where I'd often actively avoid fast travelling, but then one end of the game-world to the other could be done in the space of a few tens of minutes, less than 12 in-game hours.
I think if the game is sufficiently large, the RDR option of being able to take rides between major towns is a good one - you can enjoy the whole journey, or you can "sleep" and skip to the end. But you still only go to major hubs, not to as close to your destination as Skyrim lets you.
I also think with any fast-travel there should be the possibility of being woken up not on arrival, but by an ambush or event of sots. (A broken bridge would do just as well, forcing you to get out and cross the river some other way and continue on foot)
Sure, it makes things slower, but also more interesting.
I've heard the complete lack of fast-travel in Dragon's Dogma actually rather adds to the game-play, as long journeys can become an attrition.
Of course, there's always the view that fast-travel options don't have to be used - you could just walk the whole way, it's allowing the player to play how they want to be. But you do feel at times the game has been built a bit around having them in, expecting that the player will always use them. And they can feel a bit out-of-game experiences, as if they're an old testing shortcut rather than really built into the game.