In some of the Final Fantasy games you eventually get items that allow you to avoid some random encounters. I'm pretty sure the old Fallout games and Balder's Gate also had ways of avoiding random encounters too. Sometimes a player may want to avoid combat for whatever reason, whether they've fought that enemy alot recently, fancy a monster a bit more challenging, or something a bit easier. Giving players the ability to avoid combat shouldn't be seen as a bad feature.

And yes, running away from a battle is exactly the same as skipping it.