What is the move of this rogue in your campaign? It sounds like these encounters are starting at way too close a distance. Not a problem if the party can reasonably surpise the bad guys, but how often should that be happening?
Just remember that the rogue can sneak attack on the surpise, but he will probably have to partial charge to do it, and a partial charge only allows up to your move, not twice your move.
Try having a few bad guys with reach and combat reflexes. Combat reflexes lets you AoO even when flatfooted and the rogue has to move through threatened areas to get in his sneak attack. Sure, the rogue will still get all his sneak attacks, but it will at least come at a cost. This can be particularly dangerous to the rogue if the bad guy is a monster with reach, combat reflexes and improved grab, or maybe someone with reach, combat reflexes and improved grapple. Although it sounds like a lot, these things go so well together it is not hard to come by at all.