But if you think about it, getting attacked every time when you fast travel doesn't make sense either. I mean, villagers take the roads all the time and don't get attacked and slaughtered, the world, real or fantasy, doesn't have a danger behind every rock and bush and have these vicious blood thirsty animals just ready to pounce on you and tear you apart.
It doesn't have to be every time (that would be rather annoying, actually). It should be based on chance, and maybe some perks to help reduce that chance. The longer the trip and/or passing through wilderness, the more likely it is to happen, though. Attempt fast travel and possibly get there with no trouble, or potentially run into something you can't avoid. Or attempt to walk it, and be better prepared to avoid confrontations or sneak attack.
I just use fast travel to close the distance on trips that would be like 20 min runs from one side of the province to the other (e.g Anvil to Cheydinhal)
Ideally, something like that shouldn't happen much. The quests should be designed to not have you running all over the place, unless they were "background quests" that you don't have to specifically target (eg, the Jemane brothers have you going between Chorrol and Cheydinhal, and Chorrol and Weatherleah(sp), but you can advance them when you happen to be in the area; you don't need to run to the next target right away).