Well first of all they don't get SA on every attack. They get SA on attacks against flat-footed enemies, which pretty much limits them to the attacks they make in the first round. Ranged rogues have huge difficulties getting SA's off outside of that first round because feinting and flanking are a melee-only club. They get to be good at their job for one round of the fight.

On top of that, the rogue's BAB puts a pretty heavy restriction on how many arrows they can get off in a turn. Until level 8, they're pretty much stuck at two shots- three if they're lucky.

On top of that, the archer rogue probably won't be able to do this for every single encounter, since ranged SA's are limited to 30 feet. A ranged rogue only gets their flat-footed sneak attacks if the fight doesn't start until everyone is spitting distance from each-other, and when they do take advantage of this, they sacrifice their ability to move away from the melee enemies who are now one movement away and pissed.

On top of that, one turn of SA damage probably shouldn't be "melting" anything that wasn't already made of cotton candy. Even if you can pile on 9d6 of sneak-attack damage, that averages to about 31 points of pain. In order to secure that damage, you have to have all the above circumstances working for you, and you need to be level 5- a level at which spellcasters are ending entire encounters in one move.

So yeah, if the rogue starts a fight 30 feet away from the enemy, they have a chance at dealing a decent amount of damage to a single target during exactly one round of combat, after which they become a sub-par archer. I'm not saying that spreading out SA's isn't legit, I'm just saying that focus fire in this situation isn't some sort of game-breaking unbalanced munchkin play that must be denied.