"With a bang and a boom!"
I don't think that allowing the player to run from encounters is a bad thing, but if you find your players to be running from encounters a lot, then there's probably something wrong with your encounter rate or your combat system simply isn't fun to play (could be for various reasons: it's too slow, it's too easy/hard, annoying enemies, no variety, bad rewards).How does everyone feel about running in rpgs? Personally I've come to the decision that if you are going to let the player run you might as just let them run from encounters.
The way I did it in my game is that the only way to run from encounters is by the use of an item with a 100% success escape rate. They're just rare enough to disallow the player from running from literally every encounter, but still plentiful enough to allow them to run from any of the tougher encounters if they wish to do so.